Commit 811feb75 authored by Venkat Malladi's avatar Venkat Malladi

Add in RNA-seq RPKM data.

parent 5612e5f4
......@@ -302,6 +302,8 @@ MLK_RIP_sn_rpkm <- MLK_RIP_sn[MLK_RNA_sn_rpkm>=1 & MLK_RIP_FC>=2,]
allsno <- c(mlk_sno_rpkm_fc,mlk_sn_rpkm_fc)
allsno_rpkm <- rbind(MLK_RIP_sno_rpkm,MLK_RIP_sn_rpkm)
allsno_rna <- c(sno_tx,sn_tx)
allsno_rna_rpkm <- rbind(MLK_RNA_sno_rpkm,MLK_RNA_sn_rpkm)
# bar plot figure (B)
# Grouped Bar Plot
......@@ -412,6 +414,22 @@ 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)
allsnotx_rna <- data.frame(seqnames=seqnames(allsno_rna),
starts=start(allsno_rna)-1,
ends=end(allsno_rna),
strand=strand(allsno_rna),
tx_id = elementMetadata(allsno_rna)$tx_name,
gene_id = unlist(elementMetadata(allsno_rna)$gene_id))
allsnotx_rna_rpkm <- cbind(allsnotx_rna,allsno_rna_rpkm)
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_rna_rpkm$tx_id, gencode_sn_mapping$V2)
allsnotx_rna_rpkm$tx_name <- as.character(gencode_sn_mapping[sn_inx,"V4"])
allsnotx_rna_rpkm$gene_name <- as.character(gencode_sn_mapping[sn_inx,"V3"])
write.table(allsnotx_rna_rpkm, file="mcf-7-basal-snRNA_RPKM_RNA.tsv", quote=F, sep="\t", row.names=F, col.names=T)
# Compare PARP-1 KD to normal PARP-1 levels
MPK_RNA_counts_sno <- MPK_RNA1_counts_sno$counts + MPK_RNA2_counts_sno$counts
......@@ -606,6 +624,8 @@ MLKE_RIP_sn_rpkm <- MLKE_RIP_sn[MLKE_RNA_sn_rpkm>=1 & MLKE_RIP_FC>=2,]
mlke_allsno <- c(mlke_sno_rpkm_fc,mlke_sn_rpkm_fc)
mlke_allsno_rpkm <- rbind(MLKE_RIP_sno_rpkm,MLKE_RIP_sn_rpkm)
allsno_rna <- c(sno_tx,sn_tx)
mlke_allsno_rna_rpkm <- rbind(MLKE_RNA_sno_rpkm,MLKE_RNA_sn_rpkm)
# bar plot figure (B)
# Grouped Bar Plot
......@@ -714,6 +734,23 @@ sn_inx <- match(allsnotx_e2_rpkm$tx_id, gencode_sn_mapping$V2)
allsnotx_e2_rpkm$tx_name <- as.character(gencode_sn_mapping[sn_inx,"V4"])
allsnotx_e2_rpkm$gene_name <- as.character(gencode_sn_mapping[sn_inx,"V3"])
write.table(allsnotx_e2_rpkm, file="mcf-7-e2-snRNA_RPKM_1_FC_2.tsv", quote=F, sep="\t", row.names=F, col.names=T)
allsnotx_rna <- data.frame(seqnames=seqnames(allsno_rna),
starts=start(allsno_rna)-1,
ends=end(allsno_rna),
strand=strand(allsno_rna),
tx_id = elementMetadata(allsno_rna)$tx_name,
gene_id = unlist(elementMetadata(allsno_rna)$gene_id))
mlke_allsnotx_rna_rpkm <- cbind(allsnotx_rna,mlke_allsno_rna_rpkm)
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(mlke_allsnotx_rna_rpkm$tx_id, gencode_sn_mapping$V2)
mlke_allsnotx_rna_rpkm$tx_name <- as.character(gencode_sn_mapping[sn_inx,"V4"])
mlke_allsnotx_rna_rpkm$gene_name <- as.character(gencode_sn_mapping[sn_inx,"V3"])
write.table(mlke_allsnotx_rna_rpkm, file="mcf-7-e2-snRNA_RPKM_RNA.tsv", quote=F, sep="\t", row.names=F, col.names=T)
```
# Overlap of snoRNA and snRNA
......@@ -723,7 +760,7 @@ write.table(allsnotx_e2_rpkm, file="mcf-7-e2-snRNA_RPKM_1_FC_2.tsv", quote=F, se
basal_unique <- unique(mlk_gr_snotx$tx_name)
e2_unique <- unique(mlke_gr_snotx$tx_name)
overlap <- calculate.overlap(x = list("Basal" = basal_unique,"E2" = e2_unique))
jpeg('venndigram_basal_E2_snoRNA.jpg')
jpeg('venndigram_basal_E2_snoRNA.jpg')
draw.pairwise.venn(area1 = length(overlap$a1), area2 = length(overlap$a2), cross.area = length(overlap$a3),col = c("royalblue4", "seagreen4"),lwd=4)
dev.off()
```
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