Mercurial > repos > drosofff > repenrich

comparison edgeR_repenrich.R @ 3:1805b262c12d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ca572343d2a24d645dedd6c5d2cb352115ed8bf3
author drosofff
date Tue, 30 May 2017 10:34:53 -0400
parents 54a3f3a195d6
children
comparison
equal deleted inserted replaced
2:aed130b47d36 3:1805b262c12d
145 normalizedAbundance <- data.frame(Tag=rownames(cpm)) 145 normalizedAbundance <- data.frame(Tag=rownames(cpm))
146 normalizedAbundance <- cbind(normalizedAbundance, cpm) 146 normalizedAbundance <- cbind(normalizedAbundance, cpm)
147 write.table(normalizedAbundance, file=opt$countsfile, sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) 147 write.table(normalizedAbundance, file=opt$countsfile, sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE)
148 } 148 }
149 149
150 # test
151 print(counts)
152 print(cpm)
153
154 # Conduct fitting of the GLM 150 # Conduct fitting of the GLM
155 yfit <- glmFit(y, design) 151 yfit <- glmFit(y, design)
156 152
157 # Initialize result matrices to contain the results of the GLM 153 # Initialize result matrices to contain the results of the GLM
158 results <- matrix(nrow=dim(counts)[1],ncol=0) 154 results <- matrix(nrow=dim(counts)[1],ncol=0)
159 logfc <- matrix(nrow=dim(counts)[1],ncol=0) 155 logfc <- matrix(nrow=dim(counts)[1],ncol=0)
160 156
161 # Make the comparisons for the GLM 157 # Make the comparisons for the GLM
162 my.contrasts <- makeContrasts( 158 my.contrasts <- makeContrasts(
163 paste0(opt$levelNameB,"_",opt$levelNameA," = ", opt$levelNameB, " - ", opt$levelNameA), 159 paste0(opt$levelNameA,"_",opt$levelNameB," = ", opt$levelNameA, " - ", opt$levelNameB),
164 levels = design 160 levels = design
165 ) 161 )
166 162
167 # Define the contrasts used in the comparisons 163 # Define the contrasts used in the comparisons
168 allcontrasts = paste0(opt$levelNameB," vs ",opt$levelNameA) 164 allcontrasts = paste0(opt$levelNameA," vs ",opt$levelNameB)
169 165
170 # Conduct a for loop that will do the fitting of the GLM for each comparison 166 # Conduct a for loop that will do the fitting of the GLM for each comparison
171 # Put the results into the results objects 167 # Put the results into the results objects
172 lrt <- glmLRT(yfit, contrast=my.contrasts[,1]) 168 lrt <- glmLRT(yfit, contrast=my.contrasts[,1])
173 plotSmear(lrt, de.tags=rownames(y)) 169 plotSmear(lrt, de.tags=rownames(y))