update RNA and RIP seq analysis.

RIP-seq.Rmd

@@ -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,