Update getVariantSeq.R

Data Processing/Variant data processing/getVariantSeq.R

@@ -1,4 +1,4 @@
-getVariabntSeq <- function(dat, flankingLength){
+getVariantSeq <- function(dat, flankingLength){
  require(data.table)
  require(BSgenome.Hsapiens.UCSC.hg19)
  require(dplyr)
@@ -62,18 +62,18 @@ ncSNPs = fread(paste0(dir,ncSNPFileName,".BED")) %>% as.data.frame() %>% dplyr::
 colnames(ncSNPs) = c("Chr", "Pos", "Ref", "Alt", "Strand")
 ncSNPs$Label = "1"
 # invoke function for sequence retreival and save
-fwrite(getVariabntSeq(ncSNPs, flankingLength), file = paste0(dir, filename, "_fastaseq_Positives.csv"), sep = ",")
+fwrite(getVariantSeq(ncSNPs, flankingLength), file = paste0(dir, filename, "_", ncSNPFileName, "_fastaseq_Positives.csv"), sep = ",")
 
 
 # True Negative (i.e. non-Functional SNPs - from deepSea supple table 5)
 filename="deepsea_supple_tabale5"
 # anything other than "eQTL" is negative
-dat = as.data.frame(fread(paste0(filename, ".csv"),header = T)) %>% dplyr::filter(label != "eQTL")
+dat = fread(paste0(dir, filename, ".csv")) %>% dplyr::filter(label != "eQTL") %>% as.data.frame() 
 # dat[,8] = ifelse(dat[,8] == "eQTL",1,0)
 dat = dat[,c(2,3,4,5)]
 colnames(dat) <- c("Chr","Pos","Ref","Alt")
 dat$Label = "0"
 dat$Strand = "+"
 
 # invoke function for sequence retreival and save
-fwrite(getVariabntSeq(dat, flankingLength), file = paste0(dir, filename, "_fastaseq_Negatives.csv"), sep = ",")
+fwrite(getVariantSeq(dat, flankingLength), file = paste0(dir, filename, "_fastaseq_Negatives.csv"), sep = ",")