Mercurial > repos > artbio > gsc_mannwhitney_de
comparison MannWhitney_DE.R @ 3:3d86c89f15bf draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit fab41058cef186159d746c55808d0e69f252af2f"
| author | artbio |
|---|---|
| date | Thu, 29 Aug 2019 05:35:04 -0400 |
| parents | c67dba545a37 |
| children | 6916ac5a9ef0 |
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| 2:60964af87364 | 3:3d86c89f15bf |
|---|---|
| 136 gene_stats <- descriptive_stats(data.counts) | 136 gene_stats <- descriptive_stats(data.counts) |
| 137 | 137 |
| 138 results <- merge(gene_stats, MW_test, by = "row.names") | 138 results <- merge(gene_stats, MW_test, by = "row.names") |
| 139 colnames(results)[1] <- "genes" | 139 colnames(results)[1] <- "genes" |
| 140 | 140 |
| 141 ## Annotate Significant column | |
| 142 results$Significant[results$Significant == T & !is.na(results$Significant)] <- ifelse(subset(results, Significant == T)$log2FC > 0, "UP", "DOWN") | |
| 143 results$Significant[results$Significant == F & !is.na(results$Significant)] <- "NS" | |
| 144 | |
| 145 | |
| 141 # Save files | 146 # Save files |
| 142 write.table( | 147 write.table( |
| 143 results, | 148 results[order(results$p.adjust),], |
| 144 opt$output, | 149 opt$output, |
| 145 sep = "\t", | 150 sep = "\t", |
| 146 quote = F, | 151 quote = F, |
| 147 col.names = T, | 152 col.names = T, |
| 148 row.names = F | 153 row.names = F |