Commit f3cacb0d authored by Venkat Malladi's avatar Venkat Malladi

Testing another snoRNA host gene.

parent cc5f1360
source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")
install.packages("Rmisc")
library(SummarizedExperiment)
library(reshape2)
library(ggplot2)
library(Rmisc)
load('/Users/venkatmalladi/TCGAbiolinksGUI/TCGA-BRCA_Gene_expression_Gene_expression_quantification_hg19.rda')
load('/Users/venkatmalladi/TCGAbiolinksGUI/TCGA-BRCA_clinical.rda')
......@@ -14,7 +16,7 @@ bound$V1 <- as.character(bound$V1)
bound_gene_expression = data[rowRanges(data)$ensembl_gene_id %in% list(bound$V1)[[1]],]
bound_SNGH3 = data[rowRanges(data)$ensembl_gene_id %in% ('ENSG00000242125'),]
unbound <- read.csv("./mcf-7-basal-snoRNA_unbound_overlap_host.txt", header=F, sep='\t')
......@@ -54,6 +56,35 @@ axis(2, at=seq(-10,25,5))
dev.off()
# SNHG3
bound_rpkm <- data.frame(t(assays(bound_SNGH3)$normalized_count))
bound_rpkm['barcode'] <- rownames(bound_rpkm)
columna_data_bound <- colData(bound_SNGH3)
columna_data_bound_subest <- columna_data_bound[c('barcode',"subtype_PAM50.mRNA")]
bound_rpkm_patients <- data.frame(merge(bound_rpkm,columna_data_bound_subest,by="barcode"))
columna_data_unbound_subest <- columna_data_unbound[c('barcode',"subtype_PAM50.mRNA")]
unbound_rpkm_patients <- data.frame(merge(unbound_rpkm,columna_data_unbound_subest,by="barcode"))
bound_rpkm_patients.m <- melt(na.omit(within(bound_rpkm_patients, rm("barcode"))), id=c("subtype_PAM50.mRNA"),na.rm = TRUE)
tgc <- summarySE(bound_rpkm_patients.m, measurevar="value", groupvars=c("subtype_PAM50.mRNA"))
jpeg('barplot_SNGH3.jpg')
ggplot(tgc, aes(x=subtype_PAM50.mRNA, y=value)) +
geom_bar(position=position_dodge(), stat="identity",
colour="black", # Use black outlines,
size=.3) + # Thinner lines
geom_errorbar(aes(ymin=value-se, ymax=value+se),
size=.3, # Thinner lines
width=.2,
position=position_dodge(.9)) +
xlab("Subtype") +
ylab("FPKM") +
theme_bw()
dev.off()
# Seperate into High ESR1,FOXA1, DRAIC
......
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