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.
#source("https://bioconductor.org/biocLite.R") #biocLite("DESeq2") library(DESeq2)
# 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.