Mercurial > repos > davidecangelosi > pipe_t
comparison pipe-t.R @ 21:1e3113e565db draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit f53b88658dc1aa6627b064d7c8bed1562dfbc1dc
| author | davidecangelosi |
|---|---|
| date | Wed, 29 May 2019 05:58:58 -0400 |
| parents | 9227f7b1c50b |
| children | 822dc9b96b3e |
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| 20:9227f7b1c50b | 21:1e3113e565db |
|---|---|
| 568 width = 10*300, # 5 x 300 pixels | 568 width = 10*300, # 5 x 300 pixels |
| 569 height = 10*300, | 569 height = 10*300, |
| 570 res = 300, # 300 pixels per inch | 570 res = 300, # 300 pixels per inch |
| 571 pointsize = 8) | 571 pointsize = 8) |
| 572 | 572 |
| 573 plotCtBoxes(xFilter, cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="Ct", mar = c(8,8,8,8), names=as.character(seq(1, ncol(xFilter), 1))) # smaller font size | 573 plotCtBoxes(xFilter, ylim=c(min(exprs(xFilter), na.rm = TRUE),max(exprs(xFilter), na.rm = TRUE)), cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="Ct", mar = c(8,8,8,8), names=as.character(seq(1, ncol(xFilter), 1))) # smaller font size |
| 574 dev.off() | 574 dev.off() |
| 575 | 575 |
| 576 #write.table(exprs(xFilter), file=x, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") | 576 #write.table(exprs(xFilter), file=x, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
| 577 | 577 |
| 578 #################################################################################################################### | 578 #################################################################################################################### |
| 810 width = 10*300, # 5 x 300 pixels | 810 width = 10*300, # 5 x 300 pixels |
| 811 height = 10*300, | 811 height = 10*300, |
| 812 res = 300, # 300 pixels per inch | 812 res = 300, # 300 pixels per inch |
| 813 pointsize = 8) | 813 pointsize = 8) |
| 814 | 814 |
| 815 plotCtBoxes(normalizedDataset, cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="DeltaCt", mar = c(8,8,8,8), names=as.character(seq(1, ncol(normalizedDataset), 1))) # smaller font size | 815 plotCtBoxes(normalizedDataset, ylim=c(min(exprs(normalizedDataset), na.rm = TRUE),max(exprs(normalizedDataset),cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="DeltaCt", mar = c(8,8,8,8), names=as.character(seq(1, ncol(normalizedDataset), 1))) # smaller font size |
| 816 dev.off() | 816 dev.off() |
| 817 | 817 |
| 818 ################################################## Filtering based on number of NAs################################################## | 818 ################################################## Filtering based on number of NAs################################################## |
| 819 | 819 |
| 820 #FILTERING on the basis of NAs | 820 #FILTERING on the basis of NAs |
| 880 }, | 880 }, |
| 881 "rp"={ | 881 "rp"={ |
| 882 DEG<-RP(exprs(qFiltNAs), as.numeric(pData(qFiltNAs)$Treatment)-1, num.perm = 1000,logged = TRUE, gene.names = featureNames(qFiltNAs), huge=TRUE, plot = FALSE, rand = 123) | 882 DEG<-RP(exprs(qFiltNAs), as.numeric(pData(qFiltNAs)$Treatment)-1, num.perm = 1000,logged = TRUE, gene.names = featureNames(qFiltNAs), huge=TRUE, plot = FALSE, rand = 123) |
| 883 write.table(DEG[1:5], file=outputDEA, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") | 883 write.table(DEG[1:5], file=outputDEA, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
| 884 }, | 884 }, |
| 885 "none"={ | |
| 886 }, | |
| 885 stop("Enter something that switches me!") | 887 stop("Enter something that switches me!") |
| 886 ) | 888 ) |
| 887 | 889 |
| 888 | 890 |
| 889 cat("\n Differential expression analysis completed correctly! \n") | 891 cat("\n Differential expression analysis completed correctly! \n") |