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Author: jArloth

03_save_results_tsv.R

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+library(data.table)
+library(dplyr)
+
+exc <- function(x) setdiff(x, c('SEX', 'CHIP', paste0('C', 1:8)))
+selected <- function(e){e<-e[!is.na(e)]; exc(unique(names(unlist(sapply(e, `[[`, 'selected')))))}
+selected.single <- function(e){e<-e[!is.na(e)]; paste(exc(unique(names(e$selected))), collapse = ',')}
+
+extract.df <- function(res, features, features.uniq) {
+  
+  cutoffs <- c(0.7, 0.9)
+  pfers <- c(0.1, 1.0)
+  
+  do.call(rbind.data.frame, lapply(seq_along(res), function(i){
+    
+    cutoff <- cutoffs[i]
+    
+    l <- lapply(seq_along(res[[i]]), function(j){
+      
+      pfer <- pfers[j]
+      
+      feature.map <- data.frame(features=features,
+                                features.uniq=features.uniq,
+                                cell.line=sapply(strsplit(features, '\\|'), `[[`, 1),
+                                tf=sapply(strsplit(features, '\\|'), `[[`, 2),
+                                treatment=sapply(strsplit(features, '\\|'), `[[`, 3),
+                                hits=gsub('`', '', sapply(res[[i]][[j]], selected.single)),
+                                cutoff=cutoff,
+                                pfer=pfer,
+                                stringsAsFactors = F)
+      
+      feature.map <- transform(feature.map, hits=strsplit(hits, ',')) %>% unnest(hits)
+      feature.map
+    })
+    do.call(rbind.data.frame, l)
+  }))
+}
+
+snp.pos <- fread('MS1_functional_positions.gen', data.table=F, col.names = c('snp', 'chr', 'pos'))
+snp.pos <- unique(snp.pos)
+
+
+de1.res <- readRDS('de1-results.Rds')
+de1 <- readRDS('de1.Rds')
+de1.df <- extract.df(de1.res, de1$features, de1$features.uniq)
+de1.df <- merge(de1.df, snp.pos, by.x = 'hits', by.y='snp', all.x = T)
+write.table(de1.df, 'de1-results.tsv', row.names = F, quote = F, sep='\t')
+