modify for DA junctions

Author: kcotto

scripts/filter_and_BH.R

@@ -20,22 +20,20 @@ if (debug){
 read_file=paste("compare_junctions/hist/", "junction_pvalues", tag, ".tsv", sep="")
 regtools_data = unique(data.table::fread(file=read_file, sep = '\t', header = TRUE, stringsAsFactors = FALSE))
 regtools_data_filtered = regtools_data[(regtools_data$total_score_variant > 5 & 
-											regtools_data$pvalue >= 0 & 
-											(regtools_data$anchor == "D" | 
-												regtools_data$anchor == "A" | 
-												regtools_data$anchor == "NDA"))]
+											regtools_data$p_value_mean >= 0 & 
+											(regtools_data$anchor == "DA"))]
 
-p = regtools_data_filtered$pvalue
+p = regtools_data_filtered$p_value_mean
 adjusted_p = p.adjust(p, method = "BH")
 regtools_data_filtered$adjusted_p = adjusted_p
 regtools_data_filtered_sorted = regtools_data_filtered[order(adjusted_p)]
 
-write_file = paste("compare_junctions/hist/", "junction_pvalues_filtered_BH", tag, ".tsv", sep="")
+write_file = paste("compare_junctions/hist/", "junction_pvalues_filtered_BH_DA_junctions", tag, ".tsv", sep="")
 write.table(regtools_data_filtered_sorted, file=write_file, quote=FALSE, sep='\t', row.names = FALSE)
 
 threshold = 0.05
 is_significant = regtools_data_filtered_sorted$adjusted_p < threshold
 regtools_data_significant_filtered_sorted = regtools_data_filtered_sorted[is_significant] 
 
-write_file = paste("compare_junctions/hist/", "junction_pvalues_significant_",threshold,"_filtered_BH", tag, ".tsv", sep="")
+write_file = paste("compare_junctions/hist/", "junction_pvalues_significant_",threshold,"_filtered_BH_DA_junctions", tag, ".tsv", sep="")
 write.table(regtools_data_significant_filtered_sorted, file=write_file, quote=FALSE, sep='\t', row.names = FALSE)