Mercurial > repos > yhoogstrate > edger_with_design_matrix
comparison edgeR_Differential_Gene_Expression.xml @ 32:87bf067cfc53 draft
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| author | yhoogstrate |
|---|---|
| date | Wed, 21 May 2014 04:55:20 -0400 |
| parents | 27efc93c1ca6 |
| children | 7e45df99a6fc |
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| 31:9e9b98a1cb12 | 32:87bf067cfc53 |
|---|---|
| 245 | 245 |
| 246 ## todo EXPORT FPKM | 246 ## todo EXPORT FPKM |
| 247 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA) | 247 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA) |
| 248 | 248 |
| 249 | 249 |
| 250 if(output_MAplot != "/dev/null") { | 250 if(output_MAplot != "/dev/null" or output_PValue_distribution_plot != "/dev/null") { |
| 251 write("Creating MA plot...",stdout()) | |
| 252 | |
| 253 etable <- topTags(lrt, n=nrow(dge))\$table | 251 etable <- topTags(lrt, n=nrow(dge))\$table |
| 254 etable <- etable[order(etable\$FDR), ] | 252 etable <- etable[order(etable\$FDR), ] |
| 255 pdf(output_MAplot) | 253 |
| 256 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance")) | 254 if(output_MAplot != "/dev/null") { |
| 257 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red")) | 255 write("Creating MA plot...",stdout()) |
| 258 abline(h=c(-1,1), col="blue") | 256 pdf(output_MAplot) |
| 259 dev.off() | 257 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance")) |
| 260 } | 258 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red")) |
| 261 | 259 abline(h=c(-1,1), col="blue") |
| 262 if(output_PValue_distribution_plot != "/dev/null") { | 260 dev.off() |
| 263 write("Creating P-value distribution plot...",stdout()) | 261 } |
| 264 pdf(output_PValue_distribution_plot) | 262 |
| 265 expressed_genes <- subset(etable, PValue < 0.99) | 263 if(output_PValue_distribution_plot != "/dev/null") { |
| 266 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)") | 264 write("Creating P-value distribution plot...",stdout()) |
| 267 center <- sum(h\$counts) / length(h\$counts) | 265 pdf(output_PValue_distribution_plot) |
| 268 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2) | 266 expressed_genes <- subset(etable, PValue < 0.99) |
| 269 k <- ksmooth(h\$mid, h\$counts) | 267 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)") |
| 270 lines(k\$x,k\$y,col="red",lwd=2) | 268 center <- sum(h\$counts) / length(h\$counts) |
| 271 rmsd <- (h\$counts) - center | 269 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2) |
| 272 rmsd <- rmsd^2 | 270 k <- ksmooth(h\$mid, h\$counts) |
| 273 rmsd <- sum(rmsd) | 271 lines(k\$x,k\$y,col="red",lwd=2) |
| 274 rmsd <- sqrt(rmsd) | 272 rmsd <- (h\$counts) - center |
| 275 text(0,max(h\$counts),paste("e=",round(rmsd,2),sep=""),pos=4,col="blue") | 273 rmsd <- rmsd^2 |
| 276 ## change e into epsilon somehow | 274 rmsd <- sum(rmsd) |
| 277 dev.off() | 275 rmsd <- sqrt(rmsd) |
| 276 text(0,max(h\$counts),paste("e=",round(rmsd,2),sep=""),pos=4,col="blue") | |
| 277 ## change e into epsilon somehow | |
| 278 dev.off() | |
| 279 } | |
| 278 } | 280 } |
| 279 | 281 |
| 280 ##output_hierarchical_clustering_plot = args[13] | 282 ##output_hierarchical_clustering_plot = args[13] |
| 281 ##output_heatmap_plot = args[14] | 283 ##output_heatmap_plot = args[14] |
| 282 | 284 |