Originally posted by AddDNAse
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Loyal
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gene_diff_data<-diffData(genes(cuff_data)) sig_gene_data<-subset(gene_diff_data, (significant == 'yes')) diffGenes<-getGenes(cuff_data, sig_gene_data$gene_id) head(featureNames(diffGenes),n=3)
gene.features<-annotation(genes(cuff)) head(gene.features)
feature.level <- "genes" # ... or "isoforms", "TSS", "CDS" idColumnName <- "gene_id" # ... or "isoform_id", "TSS_group_id", "CDS_id" to match above report.name <- paste0('QC.sig_diffExp_', feature.level,'.txt') # ... or whatever you want cuff <- readCufflinks() sigIDs <- getSig(cuff,level=feature.level,alpha=0.05) if (NROW(sigIDs) > 0) { sigFeatures <- getFeatures(cuff,sigIDs,level=feature.level) sigData <- diffData(sigFeatures) sigData <- subset(sigData, (significant == 'yes')) names <- featureNames(sigFeatures) sigOutput <- merge(names, sigData, by.x="tracking_id", by.y=idColumnName) # Patch the merged table to have the original name for the ID column. # This is always the first column for the examples we've seen. colnames(sigOutput)[1] <- idColumnName write.table(sigData, report.name, sep='\t', row.names = F, col.names = T, quote = F) }
dist.selector.function <- promoters # ... or splicing or relCDS # Note that this is a function name, not a String! feature.level <- "genes" # use "isoforms" for splicing, "genes" for promoter and relCDS report.name <- "QC.sig_promoter_data.txt" # ... or whatever you want distData <- distValues(dist.selector.function(cuff)) sigData <- subset(distData, (significant == 'yes')) if (nrow(sigData) > 0) { sigIDs <- sigData[[1]] sigFeatures <- getFeatures(cuff,sigIDs,level=feature.level) names <- featureNames(sigFeatures) sigOutput <- merge(names, sigData, by.x="tracking_id", by.y=idColumnName) colnames(sigOutput)[1] <- idColumnName write.table(sigData, report.name, sep='\t', row.names = F, col.names = T, quote = F) }
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