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bioinfolec_9th_20071019

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bioinfolec_9th_20071019

  1. 1. macaque orangutan gorilla chimp human
  2. 2. 1 C C B B A A 3 2 F F G G E E D D (A) (D)
  3. 3. 1 C B A 3 2 F G G B C D E F E A D 1 2 3 (D) (C) 4
  4. 4. 4 4.1 4 10 20 30 40 1 0.74 0.76 1.34 1.75 2 2.01 2.62 0.87 0.69 3 0.87 0.60 1.83 1.90 4 1.73 1.83 0.96 0.93 4.1 10 20 30 40 4 0 5
  5. 5. > options(repos=quot;http://cran.md.tsukuba.ac.jpquot;) > install.packages(quot;apequot;) URL 'http://cran.md.tsukuba.ac.jp/bin/macosx/universal/contrib/2.6/ ape_2.0-1.tgz' Content type 'application/x-gzip' length 717872 bytes (701 Kb) URL ================================================== downloaded 701 Kb The downloaded packages are in /tmp/RtmpIFSEtI/downloaded_packages > library(ape) gee nlme lattice Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : 'gee'
  6. 6. > wm <- read.dna(quot;woodmouse.txtquot;, format=quot;fastaquot;) > wm 15 DNA sequences in binary format. > as.character(wm) $No305 [1] quot;nquot; quot;tquot; quot;tquot; quot;cquot; quot;gquot; quot;aquot; quot;aquot; quot;aquot; quot;aquot; quot;aquot; quot;cquot; quot;aquot; quot;cquot; quot;aquot; quot;cquot; quot;cquot; [18] quot;aquot; quot;cquot; quot;tquot; quot;aquot; quot;cquot; quot;tquot; quot;aquot; quot;aquot; quot;aquot; quot;aquot; quot;nquot; quot;tquot; quot;tquot; quot;aquot; quot;tquot; quot;cquot; [35] quot;gquot; quot;tquot; quot;cquot; quot;aquot; quot;cquot; quot;tquot; quot;cquot; quot;cquot; quot;tquot; quot;tquot; quot;cquot; quot;aquot; quot;tquot; quot;cquot; quot;gquot; quot;aquot; ... > names(as.character(wm)) [1] quot;No305quot; quot;No304quot; quot;No306quot; quot;No0906Squot; quot;No0908Squot; quot;No0909Squot; [7] quot;No0910Squot; quot;No0912Squot; quot;No0913Squot; quot;No1103Squot; quot;No1007Squot; quot;No1114Squot; [13] quot;No1202Squot; quot;No1206Squot; quot;No1208Squot;
  7. 7. > wm.d <- dist.dna(wm) > wm.d No305 No304 No306 No0906S No0908S No304 0.014493768 No306 0.013363824 0.003307620 No0906S 0.017879906 0.012223737 0.008860496 No0908S 0.016761346 0.011111568 0.007752093 0.012223737 No0909S 0.016743542 0.015609755 0.012223737 0.016727595 0.015609755 > wm.hc<- hclust(wm.d, quot;averagequot;) No1114S No305 No1206S No0908S > wm.phy<- as.phylo(wm.hc) No1202S No0910S No0906S No306 No304 > plot(wm.phy) No0913S No1103S No0912S No1007S No0909S No1208S
  8. 8. No0908S No1206S No305 No1202S No0910S No0906S > plot(wm.phy, type=quot;uquot;) No1114S No306 No304 > plot(wm.phy, type=quot;cquot;) No0913S No1208S No0909S No1007S No1103S No0912S No1114S No305 No1206S No0908S No1202S No0910S No0906S No306 No304 No0913S No1103S No0912S No1007S No0909S No1208S
  9. 9. X X (B) (A)
  10. 10. > wm.hc<- hclust(wm.d, quot;singlequot;) > wm.phy<- as.phylo(wm.hc) > plot(wm.phy) > wm.hc<- hclust(wm.d, quot;completequot;) > wm.phy<- as.phylo(wm.hc) > plot(wm.phy) > wm.hc<- hclust(wm.d, quot;wardquot;) > wm.phy<- as.phylo(wm.hc) > plot(wm.phy) > wm.hc<- nj(wm.d) > wm.phy<- as.phylo(wm.hc) > plot(wm.phy, type=quot;cquot;)
  11. 11. No0906S No1202S No0910S No1206S No0908S No306 No0913S No304 No1114S No305 No1007S No1208S No0909S No1103S No0912S
  12. 12. No305 No304 No306 No0906S No0908S No304 0.014493768 No306 0.013363824 0.003307620 No0906S 0.017879906 0.012223737 0.008860496 No0908S 0.016761346 0.011111568 0.007752093 0.012223737
  13. 13. wm <- read.dna(quot;woodmouse.txtquot;, format=quot;fastaquot;) wm.d <- dist.dna(wm) wm.hc<- hclust(wm.d, quot;averagequot;) wm.phy<- as.phylo(wm.hc) plot(wm.phy) > source(quot;pylo.rquot;)
  14. 14. quot;ALL1/AF4 04006quot; quot;E2A/PBX1 08018quot; quot;ALL1/AF4 15004quot;... quot;1007_s_atquot; 6.81639700357263 7.15142156514094 6.82242688637663 ... quot;1044_s_atquot; 4.57066941630317 7.01929452302597 4.89200932296006 ... quot;1065_atquot; 8.4754186077895 6.88009676843081 9.9397681802257 ...
  15. 15. > source(“http://bioconductor.org/biocLite.R”) > biocLite() ...
  16. 16. > ALLsubset <- read.table(quot;ALLsubset.txtquot;, header=T) > ALLhm <- apply(ALLsubset, c(1,2), as.numeric) > heatmap(ALLhm) > library(quot;RColorBrewerquot;) > hmcol <- colorRampPalette(brewer.pal(10,quot;RdBuquot;))(256) > heatmap(ALLhm, col=hmcol) 41401_at 41401_at 37099_at 37099_at 38717_at 38717_at 33352_at 33352_at 34308_at 34308_at 1140_at 1140_at 33777_at 33777_at 37471_at 37471_at 39003_at 39003_at 37544_at 37544_at 38413_at 38413_at 897_at 897_at 40782_at 40782_at 1065_at 1065_at 34583_at 34583_at 36638_at 36638_at 32184_at 32184_at 38994_at 38994_at 41470_at 41470_at 37809_at 37809_at 37558_at 37558_at 36873_at 36873_at 1914_at 1914_at 38063_at 38063_at 38521_at 38521_at 37475_at 37475_at 36937_s_at 36937_s_at 1389_at 1389_at 32378_at 32378_at 36452_at 36452_at 1081_at 1081_at 36203_at 36203_at 37033_s_at 37033_s_at 1988_at 1988_at 40396_at 40396_at 40365_at 40365_at 33283_at 33283_at 31901_at 31901_at 33412_at 33412_at 2059_s_at 2059_s_at 33238_at 33238_at 41275_at 41275_at 36643_at 36643_at 32529_at 32529_at 35164_at 35164_at 39781_at 39781_at 40113_at 40113_at 37343_at 37343_at 39402_at 39402_at 37981_at 37981_at 32063_at 32063_at 266_s_at 266_s_at 39829_at 39829_at 1854_at 1854_at 37625_at 37625_at 32872_at 32872_at 33355_at 33355_at 40454_at 40454_at 34800_at 34800_at 753_at 753_at 1044_s_at 1044_s_at 182_at 182_at 717_at 717_at 37493_at 37493_at 38285_at 38285_at 39614_at 39614_at 1134_at 1134_at 34897_at 34897_at 38340_at 38340_at 35260_at 35260_at 1498_at 1498_at 40235_at 40235_at 39424_at 39424_at 1007_s_at 1007_s_at 1520_s_at 1520_s_at 37579_at 37579_at 41827_f_at 41827_f_at 39318_at 39318_at 39929_at 39929_at 41139_at 41139_at 38514_at 38514_at
  17. 17. 41401_at 37099_at 38717_at 33352_at 34308_at 1140_at 33777_at 37471_at 39003_at 37544_at 38413_at 897_at 40782_at 1065_at 34583_at 36638_at 32184_at 38994_at >pdf(file=”heatmap.pdf”,pointsize=4) 41470_at 37809_at >heatmap(ALLhm) 37558_at 36873_at >dev.off() 1914_at 38063_at 38521_at 37475_at 36937_s_at 1389_at 32378_at 36452_at 1081_at 36203_at 37033_s_at 1988_at 40396_at 40365_at 33283_at 31901_at 33412_at 2059_s_at
  18. 18. > heatmap(ALLhm, hclust = function(x) hclust(x, quot;wardquot;)) > heatmap(ALLhm, hclust = function(x) hclust(x, quot;singlequot;)) 33412_at 38063_at 36638_at 38521_at 1065_at 37475_at 34583_at 1134_at 32184_at 34897_at 38994_at 38340_at 41470_at 35260_at 39003_at 1498_at 37544_at 40235_at 38413_at 897_at 897_at 36937_s_at 40782_at 37579_at 33283_at 41827_f_at 31901_at 39424_at 40365_at 1007_s_at 40396_at 2059_s_at 37033_s_at 33238_at 1988_at 41275_at 41401_at 35164_at 37099_at 39781_at 38717_at 36643_at 33352_at 32529_at 34308_at 39402_at 1140_at 40113_at 33777_at 37343_at 37471_at 37981_at 37558_at 1044_s_at 36873_at 182_at 1914_at 1081_at 37809_at 36203_at 1134_at 32378_at 34897_at 36452_at 38340_at 1389_at 35260_at 1988_at 1498_at 38285_at 40235_at 32063_at 38063_at 37493_at 38521_at 1854_at 39929_at 37475_at 41139_at 1389_at 33355_at 36937_s_at 40454_at 37579_at 34800_at 41827_f_at 753_at 32378_at 717_at 36452_at 39614_at 1081_at 1140_at 36203_at 33777_at 39929_at 37471_at 41139_at 33352_at 1520_s_at 34308_at 39318_at 37099_at 38514_at 41401_at 2059_s_at 40782_at 33238_at 38717_at 36643_at 37625_at 32529_at 32872_at 39424_at 1520_s_at 1007_s_at 39829_at 41275_at 266_s_at 39402_at 33283_at 37981_at 31901_at 40113_at 39003_at 37343_at 37033_s_at 266_s_at 37544_at 35164_at 40365_at 39781_at 1065_at 1854_at 34583_at 1044_s_at 38413_at 182_at 36638_at 37493_at 32184_at 38285_at 38994_at 39829_at 39318_at 32063_at 41470_at 37625_at 40396_at 32872_at 33412_at 33355_at 37558_at 40454_at 36873_at 717_at 37809_at 39614_at 1914_at 34800_at 38514_at 753_at
  19. 19. > library(quot;hgu95av2quot;) > library(quot;genefilterquot;) > ALLhm_gn <- ALLhm > annot <- mget(rownames(ALLhm),env=hgu95av2GENENAME) > rownames(ALLhm_gn) <- as.character(annot) > pdf(file=quot;heatmap_gn.pdfquot;,pointsize=4,width=8, paper=quot;a4quot;) > heatmap(ALLhm_gn) > dev.off()
  20. 20. 41401_at 37099_at 38717_at 33352_at 34308_at 1140_at 33777_at 37471_at 39003_at 37544_at 38413_at 897_at 40782_at 1065_at 34583_at 36638_at 32184_at 38994_at 41470_at 37809_at 37558_at 36873_at 1914_at 38063_at 38521_at 37475_at 36937_s_at 1389_at 32378_at 36452_at 1081_at 36203_at 37033_s_at 1988_at 40396_at 40365_at 33283_at 31901_at 33412_at 2059_s_at 33238_at 41275_at 36643_at 32529_at 35164_at 39781_at 40113_at 37343_at 39402_at 37981_at 32063_at 266_s_at 39829_at 1854_at 37625_at 32872_at 33355_at 40454_at 34800_at 753_at 1044_s_at 182_at 717_at 37493_at 38285_at 39614_at 1134_at 34897_at 38340_at 35260_at 1498_at 40235_at 39424_at 1007_s_at 1520_s_at 37579_at 41827_f_at 39318_at 39929_at 41139_at 38514_at

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