Zliczenia odczytów

Wykorzystamy program feature counts oraz pakiet z biblioteki Bioconductor (Rsubread)

featureCounts

featureCounts -a file.gft -g gene_name -o counts.txt  file.bam 

Rsubread

#source("https://bioconductor.org/biocLite.R")
#biocLite("Rsubread")
library(Rsubread)
HBR_1 <- "/home/bartosz/Genomika/griffith/bam/HBR_1.bam"
ann <- "/home/bartosz/Genomika/griffith/refs/ERCC92.gtf"
HBR1_fe <- featureCounts(files =HBR_1, annot.ext = ann, isGTFAnnotationFile = T)
## 
##         ==========     _____ _    _ ____  _____  ______          _____  
##         =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
##           =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
##             ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
##               ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
##         ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
##        Rsubread 1.26.1
## 
## //========================== featureCounts setting ===========================\\
## ||                                                                            ||
## ||             Input files : 1 BAM file                                       ||
## ||                           P /home/bartosz/Genomika/griffith/bam/HBR_1.bam  ||
## ||                                                                            ||
## ||      Dir for temp files : .                                                ||
## ||                 Threads : 1                                                ||
## ||                   Level : meta-feature level                               ||
## ||              Paired-end : no                                               ||
## ||         Strand specific : no                                               ||
## ||      Multimapping reads : not counted                                      ||
## || Multi-overlapping reads : not counted                                      ||
## ||   Min overlapping bases : 1                                                ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
## 
## //================================= Running ==================================\\
## ||                                                                            ||
## || Load annotation file /home/bartosz/Genomika/griffith/refs/ERCC92.gtf ...   ||
## ||    Features : 92                                                           ||
## ||    Meta-features : 92                                                      ||
## ||    Chromosomes/contigs : 92                                                ||
## ||                                                                            ||
## || Process BAM file /home/bartosz/Genomika/griffith/bam/HBR_1.bam...          ||
## ||    Paired-end reads are included.                                          ||
## ||    Assign reads to features...                                             ||
## ||    Total reads : 237142                                                    ||
## ||    Successfully assigned reads : 111944 (47.2%)                            ||
## ||    Running time : 0.01 minutes                                             ||
## ||                                                                            ||
## ||                         Read assignment finished.                          ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
HBR1_fe
## $counts
##            X.home.bartosz.Genomika.griffith.bam.HBR_1.bam
## ERCC-00002                                          37892
## ERCC-00003                                           2904
## ERCC-00004                                            910
## ERCC-00009                                            638
## ERCC-00012                                              0
## ERCC-00013                                              0
## ERCC-00014                                             26
## ERCC-00016                                              0
## ERCC-00017                                              0
## ERCC-00019                                              6
## ERCC-00022                                            298
## ERCC-00024                                              0
## ERCC-00025                                            160
## ERCC-00028                                              4
## ERCC-00031                                              0
## ERCC-00033                                              0
## ERCC-00034                                             16
## ERCC-00035                                             94
## ERCC-00039                                              2
## ERCC-00040                                              0
## ERCC-00041                                              0
## ERCC-00042                                            658
## ERCC-00043                                           1714
## ERCC-00044                                            220
## ERCC-00046                                           3154
## ERCC-00048                                              0
## ERCC-00051                                              4
## ERCC-00053                                             28
## ERCC-00054                                              4
## ERCC-00057                                              0
## ERCC-00058                                              2
## ERCC-00059                                             22
## ERCC-00060                                            186
## ERCC-00061                                              0
## ERCC-00062                                             26
## ERCC-00067                                              0
## ERCC-00069                                              2
## ERCC-00071                                             78
## ERCC-00073                                              2
## ERCC-00074                                          20982
## ERCC-00075                                              0
## ERCC-00076                                            198
## ERCC-00077                                              2
## ERCC-00078                                             82
## ERCC-00079                                             56
## ERCC-00081                                              0
## ERCC-00083                                              0
## ERCC-00084                                             54
## ERCC-00085                                              4
## ERCC-00086                                              0
## ERCC-00092                                             66
## ERCC-00095                                             40
## ERCC-00096                                          20708
## ERCC-00097                                              0
## ERCC-00098                                              0
## ERCC-00099                                             36
## ERCC-00104                                              0
## ERCC-00108                                            218
## ERCC-00109                                              0
## ERCC-00111                                           1046
## ERCC-00112                                            360
## ERCC-00113                                           7096
## ERCC-00116                                            300
## ERCC-00117                                              0
## ERCC-00120                                              2
## ERCC-00123                                              0
## ERCC-00126                                              6
## ERCC-00130                                           8088
## ERCC-00131                                             38
## ERCC-00134                                              0
## ERCC-00136                                            518
## ERCC-00137                                              0
## ERCC-00138                                              2
## ERCC-00142                                              0
## ERCC-00143                                              0
## ERCC-00144                                              2
## ERCC-00145                                            974
## ERCC-00147                                              0
## ERCC-00148                                              2
## ERCC-00150                                              0
## ERCC-00154                                              2
## ERCC-00156                                              0
## ERCC-00157                                             22
## ERCC-00158                                              0
## ERCC-00160                                             16
## ERCC-00162                                             56
## ERCC-00163                                             10
## ERCC-00164                                              0
## ERCC-00165                                             66
## ERCC-00168                                              4
## ERCC-00170                                              2
## ERCC-00171                                           1836
## 
## $annotation
##        GeneID        Chr Start  End Strand Length
## 1  ERCC-00002 ERCC-00002     1 1061      +   1061
## 2  ERCC-00003 ERCC-00003     1 1023      +   1023
## 3  ERCC-00004 ERCC-00004     1  523      +    523
## 4  ERCC-00009 ERCC-00009     1  984      +    984
## 5  ERCC-00012 ERCC-00012     1  994      +    994
## 6  ERCC-00013 ERCC-00013     1  808      +    808
## 7  ERCC-00014 ERCC-00014     1 1957      +   1957
## 8  ERCC-00016 ERCC-00016     1  844      +    844
## 9  ERCC-00017 ERCC-00017     1 1136      +   1136
## 10 ERCC-00019 ERCC-00019     1  644      +    644
## 11 ERCC-00022 ERCC-00022     1  751      +    751
## 12 ERCC-00024 ERCC-00024     1  536      +    536
## 13 ERCC-00025 ERCC-00025     1 1994      +   1994
## 14 ERCC-00028 ERCC-00028     1 1130      +   1130
## 15 ERCC-00031 ERCC-00031     1 1138      +   1138
## 16 ERCC-00033 ERCC-00033     1 2022      +   2022
## 17 ERCC-00034 ERCC-00034     1 1019      +   1019
## 18 ERCC-00035 ERCC-00035     1 1130      +   1130
## 19 ERCC-00039 ERCC-00039     1  740      +    740
## 20 ERCC-00040 ERCC-00040     1  744      +    744
## 21 ERCC-00041 ERCC-00041     1 1122      +   1122
## 22 ERCC-00042 ERCC-00042     1 1023      +   1023
## 23 ERCC-00043 ERCC-00043     1 1023      +   1023
## 24 ERCC-00044 ERCC-00044     1 1156      +   1156
## 25 ERCC-00046 ERCC-00046     1  522      +    522
## 26 ERCC-00048 ERCC-00048     1  992      +    992
## 27 ERCC-00051 ERCC-00051     1  274      +    274
## 28 ERCC-00053 ERCC-00053     1 1023      +   1023
## 29 ERCC-00054 ERCC-00054     1  274      +    274
## 30 ERCC-00057 ERCC-00057     1 1021      +   1021
## 31 ERCC-00058 ERCC-00058     1 1136      +   1136
## 32 ERCC-00059 ERCC-00059     1  525      +    525
## 33 ERCC-00060 ERCC-00060     1  523      +    523
## 34 ERCC-00061 ERCC-00061     1 1136      +   1136
## 35 ERCC-00062 ERCC-00062     1 1023      +   1023
## 36 ERCC-00067 ERCC-00067     1  644      +    644
## 37 ERCC-00069 ERCC-00069     1 1137      +   1137
## 38 ERCC-00071 ERCC-00071     1  642      +    642
## 39 ERCC-00073 ERCC-00073     1  603      +    603
## 40 ERCC-00074 ERCC-00074     1  522      +    522
## 41 ERCC-00075 ERCC-00075     1 1023      +   1023
## 42 ERCC-00076 ERCC-00076     1  642      +    642
## 43 ERCC-00077 ERCC-00077     1  273      +    273
## 44 ERCC-00078 ERCC-00078     1  993      +    993
## 45 ERCC-00079 ERCC-00079     1  644      +    644
## 46 ERCC-00081 ERCC-00081     1  534      +    534
## 47 ERCC-00083 ERCC-00083     1 1022      +   1022
## 48 ERCC-00084 ERCC-00084     1  994      +    994
## 49 ERCC-00085 ERCC-00085     1  844      +    844
## 50 ERCC-00086 ERCC-00086     1 1020      +   1020
## 51 ERCC-00092 ERCC-00092     1 1124      +   1124
## 52 ERCC-00095 ERCC-00095     1  521      +    521
## 53 ERCC-00096 ERCC-00096     1 1107      +   1107
## 54 ERCC-00097 ERCC-00097     1  523      +    523
## 55 ERCC-00098 ERCC-00098     1 1143      +   1143
## 56 ERCC-00099 ERCC-00099     1 1350      +   1350
## 57 ERCC-00104 ERCC-00104     1 2022      +   2022
## 58 ERCC-00108 ERCC-00108     1 1022      +   1022
## 59 ERCC-00109 ERCC-00109     1  536      +    536
## 60 ERCC-00111 ERCC-00111     1  994      +    994
## 61 ERCC-00112 ERCC-00112     1 1136      +   1136
## 62 ERCC-00113 ERCC-00113     1  840      +    840
## 63 ERCC-00116 ERCC-00116     1 1991      +   1991
## 64 ERCC-00117 ERCC-00117     1 1136      +   1136
## 65 ERCC-00120 ERCC-00120     1  536      +    536
## 66 ERCC-00123 ERCC-00123     1 1022      +   1022
## 67 ERCC-00126 ERCC-00126     1 1118      +   1118
## 68 ERCC-00130 ERCC-00130     1 1059      +   1059
## 69 ERCC-00131 ERCC-00131     1  771      +    771
## 70 ERCC-00134 ERCC-00134     1  274      +    274
## 71 ERCC-00136 ERCC-00136     1 1033      +   1033
## 72 ERCC-00137 ERCC-00137     1  537      +    537
## 73 ERCC-00138 ERCC-00138     1 1024      +   1024
## 74 ERCC-00142 ERCC-00142     1  493      +    493
## 75 ERCC-00143 ERCC-00143     1  784      +    784
## 76 ERCC-00144 ERCC-00144     1  538      +    538
## 77 ERCC-00145 ERCC-00145     1 1042      +   1042
## 78 ERCC-00147 ERCC-00147     1 1023      +   1023
## 79 ERCC-00148 ERCC-00148     1  494      +    494
## 80 ERCC-00150 ERCC-00150     1  743      +    743
## 81 ERCC-00154 ERCC-00154     1  537      +    537
## 82 ERCC-00156 ERCC-00156     1  494      +    494
## 83 ERCC-00157 ERCC-00157     1 1019      +   1019
## 84 ERCC-00158 ERCC-00158     1 1027      +   1027
## 85 ERCC-00160 ERCC-00160     1  743      +    743
## 86 ERCC-00162 ERCC-00162     1  523      +    523
## 87 ERCC-00163 ERCC-00163     1  543      +    543
## 88 ERCC-00164 ERCC-00164     1 1022      +   1022
## 89 ERCC-00165 ERCC-00165     1  872      +    872
## 90 ERCC-00168 ERCC-00168     1 1024      +   1024
## 91 ERCC-00170 ERCC-00170     1 1023      +   1023
## 92 ERCC-00171 ERCC-00171     1  505      +    505
## 
## $targets
## [1] "X.home.bartosz.Genomika.griffith.bam.HBR_1.bam"
## 
## $stat
##                           Status
## 1                       Assigned
## 2            Unassigned_Unmapped
## 3      Unassigned_MappingQuality
## 4             Unassigned_Chimera
## 5      Unassigned_FragmentLength
## 6           Unassigned_Duplicate
## 7        Unassigned_MultiMapping
## 8           Unassigned_Secondary
## 9         Unassigned_Nonjunction
## 10         Unassigned_NoFeatures
## 11 Unassigned_Overlapping_Length
## 12          Unassigned_Ambiguity
##    X.home.bartosz.Genomika.griffith.bam.HBR_1.bam
## 1                                          111944
## 2                                          125198
## 3                                               0
## 4                                               0
## 5                                               0
## 6                                               0
## 7                                               0
## 8                                               0
## 9                                               0
## 10                                              0
## 11                                              0
## 12                                              0

Zadanie 1:
Wykonać macierz "count_matrix.txt" zawierającą liczby odczytów dla poszczególnych genów z dla wszystkich plików bam utworzonych na poprzednich ćwiczeniach.

DESeq2 - normalizacja danych

#source("https://bioconductor.org/biocLite.R")
#biocLite("DESeq2")
library(DESeq2)
## Loading required package: S4Vectors
## Loading required package: stats4
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, cbind, colMeans,
##     colnames, colSums, do.call, duplicated, eval, evalq, Filter,
##     Find, get, grep, grepl, intersect, is.unsorted, lapply,
##     lengths, Map, mapply, match, mget, order, paste, pmax,
##     pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
##     rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
##     tapply, union, unique, unsplit, which, which.max, which.min
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:base':
## 
##     expand.grid
## Loading required package: IRanges
## Loading required package: GenomicRanges
## Loading required package: GenomeInfoDb
## Loading required package: SummarizedExperiment
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: DelayedArray
## Loading required package: matrixStats
## 
## Attaching package: 'matrixStats'
## The following objects are masked from 'package:Biobase':
## 
##     anyMissing, rowMedians
## 
## Attaching package: 'DelayedArray'
## The following objects are masked from 'package:matrixStats':
## 
##     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
## The following object is masked from 'package:base':
## 
##     apply
# dane
countData
##            bam.HBR_1.bam bam.HBR_2.bam bam.HBR_3.bam bam.UHR_1.bam
## ERCC-00002         37892         47257         42234         39986
## ERCC-00003          2904          3170          3038          3488
## ERCC-00004           910          1078           996          9200
## ERCC-00009           638           778           708          1384
## ERCC-00012             0             0             0             2
## ERCC-00013             0             0             0             4
## ERCC-00014            26            20             8            20
## ERCC-00016             0             0             0             0
## ERCC-00017             0             0             0             0
## ERCC-00019             6            10             4            26
## ERCC-00022           298           327           326           402
## ERCC-00024             0             0             0             0
## ERCC-00025           160           158           120           266
## ERCC-00028             4             0             0            12
## ERCC-00031             0             2             8             8
## ERCC-00033             0             0             0             0
## ERCC-00034            16            32            24            38
## ERCC-00035            94           156           114           256
## ERCC-00039             2             2             6             8
## ERCC-00040             0             0             0             0
## ERCC-00041             0             2             2             0
## ERCC-00042           658           758           682          1462
## ERCC-00043          1714          1958          1848          2178
## ERCC-00044           220           324           242           360
## ERCC-00046          3154          3346          3166          3814
## ERCC-00048             0             0             0             0
## ERCC-00051             4             0             4            18
## ERCC-00053            28            34            22            54
## ERCC-00054             4             4             6             6
## ERCC-00057             0             0             0             0
## ERCC-00058             2            14            10             2
## ERCC-00059            22            16            30            28
## ERCC-00060           186           204           200           474
## ERCC-00061             0             0             0             0
## ERCC-00062            26            24             8           194
## ERCC-00067             0             0             4             2
## ERCC-00069             2            12             8             6
## ERCC-00071            78            96            64           134
## ERCC-00073             2             0             0             2
## ERCC-00074         20982         24826         22956         31394
## ERCC-00075             0             0             0             0
## ERCC-00076           198           282           242           255
## ERCC-00077             2             0             0             0
## ERCC-00078            82           100           110            90
## ERCC-00079            56            78            96            90
## ERCC-00081             0             0             0             0
## ERCC-00083             0             0             0             0
## ERCC-00084            54            68            82            92
## ERCC-00085             4             4             0            24
## ERCC-00086             0             0             0             0
## ERCC-00092            66           110            82           700
## ERCC-00095            40            60            40           330
## ERCC-00096         20708         25719         22637         44015
## ERCC-00097             0             0             0             4
## ERCC-00098             0             0             0             0
## ERCC-00099            36            34            22            32
## ERCC-00104             0             0             2             0
## ERCC-00108           218           222           250          1846
## ERCC-00109             0             0             0             0
## ERCC-00111          1046          1254           996          1320
## ERCC-00112           360           488           444           428
## ERCC-00113          7096          8594          7779          9868
## ERCC-00116           300           288           286          2050
## ERCC-00117             0             0             0             0
## ERCC-00120             2             0             0             0
## ERCC-00123             0             0             0             0
## ERCC-00126             6             6            10            26
## ERCC-00130          8088         10680          8766         69799
## ERCC-00131            38            72            40           306
## ERCC-00134             0             0             2             0
## ERCC-00136           518           604           486          4448
## ERCC-00137             0             0             0             2
## ERCC-00138             2             0             0             0
## ERCC-00142             0             0             0             0
## ERCC-00143             0             6             2             8
## ERCC-00144             2             2             8            20
## ERCC-00145           974          1380          1118          1548
## ERCC-00147             0             0             0             0
## ERCC-00148             2             0            10             6
## ERCC-00150             0             6             2             4
## ERCC-00154             2             0             2             2
## ERCC-00156             0             0             0             0
## ERCC-00157            22            18            30            26
## ERCC-00158             0             0             4             2
## ERCC-00160            16            42            28            26
## ERCC-00162            56            44            54           100
## ERCC-00163            10            14            26            12
## ERCC-00164             0             2             0             0
## ERCC-00165            66           128            82           102
## ERCC-00168             4             2             2             0
## ERCC-00170             2             4             6            36
## ERCC-00171          1836          2510          2116          3814
##            bam.UHR_2.bam bam.UHR_3.bam
## ERCC-00002         25978         33998
## ERCC-00003          2201          2680
## ERCC-00004          6678          7395
## ERCC-00009           954          1108
## ERCC-00012             0             0
## ERCC-00013             4             0
## ERCC-00014             4            16
## ERCC-00016             0             0
## ERCC-00017             0             2
## ERCC-00019            22            24
## ERCC-00022           198           306
## ERCC-00024             0             0
## ERCC-00025           194           216
## ERCC-00028            16            10
## ERCC-00031             0             0
## ERCC-00033             0             6
## ERCC-00034            14            36
## ERCC-00035           130           202
## ERCC-00039             6             2
## ERCC-00040             0             2
## ERCC-00041             0             0
## ERCC-00042          1062          1346
## ERCC-00043          1450          1736
## ERCC-00044           206           256
## ERCC-00046          2504          2938
## ERCC-00048             0             0
## ERCC-00051            10             4
## ERCC-00053            58            70
## ERCC-00054             0             2
## ERCC-00057             0             0
## ERCC-00058             6             6
## ERCC-00059            14            12
## ERCC-00060           334           336
## ERCC-00061             0             0
## ERCC-00062           114           160
## ERCC-00067             0             4
## ERCC-00069             2             2
## ERCC-00071            64           100
## ERCC-00073             2             0
## ERCC-00074         23242         26375
## ERCC-00075             0             0
## ERCC-00076           150           194
## ERCC-00077             4             2
## ERCC-00078            50            64
## ERCC-00079            56            68
## ERCC-00081             0             0
## ERCC-00083             0             0
## ERCC-00084            50            60
## ERCC-00085             4            22
## ERCC-00086             0             0
## ERCC-00092           512           612
## ERCC-00095           224           250
## ERCC-00096         28870         36412
## ERCC-00097             0             0
## ERCC-00098             0             0
## ERCC-00099            26            40
## ERCC-00104             4             0
## ERCC-00108          1228          1667
## ERCC-00109             4             0
## ERCC-00111           962          1110
## ERCC-00112           316           326
## ERCC-00113          6686          8543
## ERCC-00116          1418          2014
## ERCC-00117             0             0
## ERCC-00120             0             0
## ERCC-00123             0             0
## ERCC-00126             4            22
## ERCC-00130         44902         57165
## ERCC-00131           182           268
## ERCC-00134             0             0
## ERCC-00136          3060          3600
## ERCC-00137             4             0
## ERCC-00138             2             0
## ERCC-00142             2             0
## ERCC-00143            10             6
## ERCC-00144            10             8
## ERCC-00145           982          1216
## ERCC-00147             0             0
## ERCC-00148             2            10
## ERCC-00150             8             0
## ERCC-00154            14             8
## ERCC-00156             0             0
## ERCC-00157            24            24
## ERCC-00158             2             4
## ERCC-00160            18            20
## ERCC-00162            74            66
## ERCC-00163             8            18
## ERCC-00164             0             0
## ERCC-00165            56            74
## ERCC-00168             2             0
## ERCC-00170            28            30
## ERCC-00171          2674          3318
samples = names(countData)

cond_1 = rep("cond1", 3)
cond_2 = rep("cond2", 3)
condition = factor(c(cond_1, cond_2))
colData = data.frame(samples=samples, condition=condition)
dds = DESeqDataSetFromMatrix(countData=countData, colData=colData, design = ~condition)
dss1 <- estimateSizeFactors(dds)
dss1$sizeFactor
## bam.HBR_1.bam bam.HBR_2.bam bam.HBR_3.bam bam.UHR_1.bam bam.UHR_2.bam 
##     0.7217514     1.0028739     0.9217573     1.4708414     0.8689237 
## bam.UHR_3.bam 
##     1.2011701
log_data <- rlog(dds)
norm_data<-assay(log_data)
norm_data <- as.data.frame(norm_data)
norm_data
##            bam.HBR_1.bam bam.HBR_2.bam bam.HBR_3.bam bam.UHR_1.bam
## ERCC-00002   15.52705953   15.41808227   15.38998948   14.88111723
## ERCC-00003   11.82076527   11.58296943   11.62414630   11.30493923
## ERCC-00004   10.72045617   10.58126251   10.58587376   12.27776171
## ERCC-00009    9.79222594    9.66683405    9.65743700    9.85304387
## ERCC-00012   -1.54022708   -1.54935372   -1.54701359   -1.45420315
## ERCC-00013   -0.01216674   -0.02254289   -0.02002599    0.27463446
## ERCC-00014    4.50195130    4.05860727    3.55724499    3.80442222
## ERCC-00016    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00017   -1.49272487   -1.50357255   -1.50079115   -1.51549637
## ERCC-00019    3.47982887    3.56198236    3.21233234    3.91209208
## ERCC-00022    8.53966816    8.31260187    8.39074001    8.14492412
## ERCC-00024    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00025    7.68758527    7.36703671    7.19494836    7.49498423
## ERCC-00028    2.46725915    1.93389025    1.94492112    2.65337025
## ERCC-00031    0.95079333    1.15431259    1.66283359    1.46445235
## ERCC-00033   -0.60638948   -0.61664256   -0.61484250   -0.62389142
## ERCC-00034    4.55939696    4.82714592    4.67289597    4.66775363
## ERCC-00035    7.09773174    7.26012528    7.05096942    7.36576016
## ERCC-00039    1.91301018    1.83665790    2.18547128    2.11960212
## ERCC-00040   -1.49272487   -1.50357255   -1.50079115   -1.51549637
## ERCC-00041   -0.69247089   -0.49355604   -0.47945628   -0.70978047
## ERCC-00042    9.84826155    9.66870068    9.64861133    9.93237818
## ERCC-00043   11.08495411   10.89222849   10.91828537   10.62512532
## ERCC-00044    8.17735219    8.23360380    8.03502926    7.96868418
## ERCC-00046   11.93924849   11.67332866   11.70189168   11.42955472
## ERCC-00048    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00051    2.46111856    1.95014415    2.37171561    2.86734313
## ERCC-00053    5.31643535    5.20947641    4.95293450    5.27059649
## ERCC-00054    1.92343617    1.81574090    1.99478100    1.82562505
## ERCC-00057    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00058    2.37312550    3.04834520    2.89679037    2.19628379
## ERCC-00059    4.61011140    4.15571458    4.66627539    4.27149935
## ERCC-00060    8.03598660    7.81912926    7.87708626    8.24935259
## ERCC-00061    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00062    5.46213146    5.15157336    4.58172504    6.62519340
## ERCC-00067    0.32987247    0.31750124    0.72785821    0.46720923
## ERCC-00069    2.10051286    2.68879424    2.51099431    2.19809148
## ERCC-00071    6.63144171    6.52266524    6.24119443    6.47843645
## ERCC-00073    0.13209225   -0.14168322   -0.13950424    0.01125556
## ERCC-00074   14.75232528   14.59385406   14.59976890   14.44995666
## ERCC-00075    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00076    7.98193741    8.00657043    7.93986015    7.54859789
## ERCC-00077    0.53137604    0.24818380    0.25122320    0.23596232
## ERCC-00078    6.64191061    6.52276831    6.68955463    6.09004094
## ERCC-00079    6.23770451    6.24036892    6.50521857    6.03094460
## ERCC-00081    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00083    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00084    6.15290150    6.06764169    6.30713276    5.99768311
## ERCC-00085    2.70023301    2.57517881    2.19454123    3.28839668
## ERCC-00086    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00092    7.04570929    7.19101673    7.01918268    8.57736397
## ERCC-00095    6.21954643    6.27478252    6.02499588    7.48948048
## ERCC-00096   14.80674743   14.69747911   14.65584672   14.84811276
## ERCC-00097   -1.08939655   -1.10548354   -1.10135875   -0.84578586
## ERCC-00098    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00099    5.33995234    5.02735277    4.76542836    4.69442298
## ERCC-00104   -0.17177298   -0.18157728    0.05856094   -0.19117155
## ERCC-00108    8.61043878    8.34249988    8.51546083    9.98475990
## ERCC-00109   -0.75761336   -0.77279497   -0.77110312   -0.77962311
## ERCC-00111   10.37519579   10.23036565   10.08780941    9.91050644
## ERCC-00112    8.84445693    8.82044343    8.81039029    8.32863666
## ERCC-00113   13.16907421   13.03338527   13.01832870   12.79571433
## ERCC-00116    8.99647466    8.67207259    8.73846786   10.17062142
## ERCC-00117    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00120   -1.30185745   -1.51660819   -1.51242408   -1.53495238
## ERCC-00123    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00126    3.26258934    3.11182973    3.39588077    3.70273840
## ERCC-00130   13.81969518   13.77415098   13.67438306   15.22915348
## ERCC-00131    6.16911277    6.41664336    6.01475110    7.40444712
## ERCC-00134   -1.49481121   -1.50829305   -1.34089550   -1.52300021
## ERCC-00136    9.84224077    9.68704466    9.57293241   11.24409329
## ERCC-00137   -0.31427271   -0.32291111   -0.32081516   -0.16245480
## ERCC-00138   -0.26593822   -0.54803697   -0.54625545   -0.55518765
## ERCC-00142   -1.49660813   -1.51073880   -1.50711562   -1.52636087
## ERCC-00143    1.80943918    2.30697188    2.00545820    2.27160029
## ERCC-00144    2.51466225    2.42518822    2.91135763    3.17180553
## ERCC-00145   10.33652921   10.35574226   10.23206180   10.09478300
## ERCC-00147    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00148    1.96741974    1.67357389    2.49929898    2.07005706
## ERCC-00150    1.25879364    1.78582795    1.47212317    1.52208019
## ERCC-00154    1.86855926    1.55400381    1.80523583    1.69874741
## ERCC-00156    0.00000000    0.00000000    0.00000000    0.00000000
## ERCC-00157    4.75387311    4.37866010    4.80741076    4.36404441
## ERCC-00158    0.65803902    0.64304408    1.04755887    0.78760341
## ERCC-00160    4.52687169    5.01726263    4.75811807    4.36695856
## ERCC-00162    6.16272555    5.68092811    5.91919625    6.04784480
## ERCC-00163    3.79734497    3.80182798    4.28778841    3.49881669
## ERCC-00164   -1.49542288   -1.35487234   -1.50478771   -1.52200602
## ERCC-00165    6.45159195    6.76156737    6.42736053    6.20695479
## ERCC-00168    1.12418793    0.84411836    0.86051029    0.61044840
## ERCC-00170    3.08953189    3.15278997    3.34378860    4.15369180
## ERCC-00171   11.32644756   11.31062807   11.22721191   11.34513997
##            bam.UHR_2.bam bam.UHR_3.bam
## ERCC-00002   14.97165547   14.91938837
## ERCC-00003   11.36759749   11.24792520
## ERCC-00004   12.49523456   12.26110118
## ERCC-00009   10.00405785    9.83363773
## ERCC-00012   -1.54537589   -1.55435969
## ERCC-00013    0.41614925   -0.02757783
## ERCC-00014    3.29884760    3.79202711
## ERCC-00016    0.00000000    0.00000000
## ERCC-00017   -1.49884461   -1.37761348
## ERCC-00019    4.16045812    3.99494120
## ERCC-00022    7.97894434    8.07964283
## ERCC-00024    0.00000000    0.00000000
## ERCC-00025    7.69481091    7.48964852
## ERCC-00028    3.13656998    2.66044325
## ERCC-00031    0.93828532    0.91864674
## ERCC-00033   -0.61354072   -0.11399355
## ERCC-00034    4.34918042    4.77985920
## ERCC-00035    7.22395179    7.33321308
## ERCC-00039    2.20914828    1.79891049
## ERCC-00040   -1.49884461   -1.37761348
## ERCC-00041   -0.70160241   -0.70692266
## ERCC-00042   10.13659200   10.05033116
## ERCC-00043   10.73922387   10.60234397
## ERCC-00044    7.93909714    7.84052943
## ERCC-00046   11.53048401   11.37475548
## ERCC-00048    0.00000000    0.00000000
## ERCC-00051    2.81384640    2.28269858
## ERCC-00053    5.77542257    5.65841047
## ERCC-00054    1.44511022    1.60680567
## ERCC-00057    0.00000000    0.00000000
## ERCC-00058    2.66965329    2.53575493
## ERCC-00059    4.16347738    3.87856594
## ERCC-00060    8.41840433    8.11348731
## ERCC-00061    0.00000000    0.00000000
## ERCC-00062    6.61466877    6.63323560
## ERCC-00067    0.32266887    0.65462923
## ERCC-00069    2.05293787    1.97729923
## ERCC-00071    6.29151430    6.39772671
## ERCC-00073    0.09684099   -0.14603171
## ERCC-00074   14.67003642   14.47720163
## ERCC-00075    0.00000000    0.00000000
## ERCC-00076    7.54564141    7.48427776
## ERCC-00077    0.68731352    0.43536337
## ERCC-00078    6.04181570    5.97549269
## ERCC-00079    6.07678250    5.96576979
## ERCC-00081    0.00000000    0.00000000
## ERCC-00083    0.00000000    0.00000000
## ERCC-00084    5.92799485    5.81060609
## ERCC-00085    2.62817643    3.36096273
## ERCC-00086    0.00000000    0.00000000
## ERCC-00092    8.79700836    8.64707799
## ERCC-00095    7.62680689    7.41370488
## ERCC-00096   14.95137580   14.86082194
## ERCC-00097   -1.09847206   -1.11001554
## ERCC-00098    0.00000000    0.00000000
## ERCC-00099    4.93103432    5.01369762
## ERCC-00104    0.26737259   -0.18634948
## ERCC-00108   10.10790199   10.08928332
## ERCC-00109   -0.31060924   -0.77618872
## ERCC-00111   10.11139081    9.93806287
## ERCC-00112    8.53848408    8.26468271
## ERCC-00113   12.92782419   12.85157013
## ERCC-00116   10.33386780   10.36247827
## ERCC-00117    0.00000000    0.00000000
## ERCC-00120   -1.50949588   -1.52555880
## ERCC-00123    0.00000000    0.00000000
## ERCC-00126    3.02182913    3.72312869
## ERCC-00130   15.31839586   15.23213656
## ERCC-00131    7.40861755    7.47339648
## ERCC-00134   -1.50241702   -1.51568786
## ERCC-00136   11.40374036   11.23464534
## ERCC-00137    0.12072816   -0.32710474
## ERCC-00138   -0.30110183   -0.55159891
## ERCC-00142   -1.33274937   -1.51848949
## ERCC-00143    2.62170882    2.23729675
## ERCC-00144    3.05989318    2.78799298
## ERCC-00145   10.16337988   10.05777334
## ERCC-00147    0.00000000    0.00000000
## ERCC-00148    1.92110073    2.36865154
## ERCC-00150    1.98323471    1.22050806
## ERCC-00154    2.67780309    2.18304411
## ERCC-00156    0.00000000    0.00000000
## ERCC-00157    4.68130366    4.44887711
## ERCC-00158    0.87913615    0.97368420
## ERCC-00160    4.47927514    4.33010724
## ERCC-00162    6.24741587    5.86434460
## ERCC-00163    3.57267705    3.84639785
## ERCC-00164   -1.50252781   -1.51492472
## ERCC-00165    6.14615973    6.10622571
## ERCC-00168    0.87232140    0.61840539
## ERCC-00170    4.35843591    4.16522099
## ERCC-00171   11.51341041   11.40706267

Zadanie 2:
Wykonać heat mapę z clastrowaniem genów i próbek dla genów o wysokiej eskpresji.