Commit 35a0c84f authored by Venkat Malladi's avatar Venkat Malladi

update RNA and RIP seq analysis.

parent ffbc5450
......@@ -400,21 +400,21 @@ typeTesting <-matrix(c(63,19,38,76),nrow = 2,dimnames = list(Guess = c("bound",
fisher.test(typeTesting)
# Combine snRNA and snoRNA and print out
allsnotx <- data.frame(seqnames=seqnames(allsno),
starts=start(allsno)-1,
ends=end(allsno),
strand=strand(allsno),
tx_id = elementMetadata(allsno)$tx_name,
gene_id = unlist(elementMetadata(allsno)$gene_id))
allsnotx_rpkm <- cbind(allsnotx,allsno_rpkm)
allsnotx <- data.frame(seqnames=seqnames(test),
starts=start(test)-1,
ends=end(test),
strand=strand(test),
tx_id = elementMetadata(test)$tx_name,
gene_id = unlist(elementMetadata(test)$gene_id))
allsnotx_rpkm <- cbind(allsnotx,test_2)
sno_mapping <- read.csv("./gencode.v19.annotation_snoRNA_mapping.txt", header=F, sep=',')
sn_mapping <- read.csv("./gencode.v19.annotation_snRNA_mapping.txt", header=F, sep=',')
gencode_sn_mapping <-rbind(sno_mapping,sn_mapping)
sn_inx <- match(allsnotx_rpkm$tx_id, gencode_sn_mapping$V2)
allsnotx_rpkm$tx_name <- as.character(gencode_sn_mapping[sn_inx,"V4"])
allsnotx_rpkm$gene_name <- as.character(gencode_sn_mapping[sn_inx,"V3"])
write.table(allsnotx_rpkm, file="mcf-7-basal-snRNA_RPKM_1_FC_2.tsv", quote=F, sep="\t", row.names=F, col.names=T)
write.table(allsnotx_rpkm, file="mcf-7-basal-snRNAtest.tsv", quote=F, sep="\t", row.names=F, col.names=T)
allsnotx_rna <- data.frame(seqnames=seqnames(allsno_rna),
starts=start(allsno_rna)-1,
......
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