edgeR_analysis

library(edgeR)
setwd("/home/chengchen/data/DBA_project/rpl11")

count <- read.delim("rpl11-countmatrix.txt")
colnames(count) = c("geneid","control","rpl11mo")
rownames(count) = count$geneid
count= count[,2:3]

bcv <- 0.2
y <- DGEList(counts=count, group=1:2)
keep <- rowSums(cpm(y)>1) >= 1
y <- y[keep, , keep.lib.sizes=FALSE]
y <- calcNormFactors(y)

y_bca = y
bcv = 0.1
et = exactTest(y_bca,dispersion = bcv^2)

allgenes = et$table
allgenes= allgenes[order(allgenes$PValue),]

ids = rownames(allgenes)
###get zfin_gene_symbol for ensembl genes
library("biomaRt")
ensembl=useMart("ensembl")
ensembl=useDataset("drerio_gene_ensembl",mart=ensembl)
symbols <- getBM(attributes=c('ensembl_gene_id','entrezgene_id','zfin_id_symbol', 'wikigene_description','name_1006'),filters='ensembl_gene_id',values=ids, mart=ensembl)
#entrezgene is ENTREZID
symbols=symbols[!duplicated(symbols$ensembl_gene_id),]
res05_lfc = as.data.frame(allgenes)
res05_lfc$ensembl_gene_id = rownames(res05_lfc)
res05_lfc = merge(res05_lfc,symbols, by="ensembl_gene_id")
#res05_lfc=res05_lfc[,-7] #remove ensembl_gene_id column
res05_lfc_ordered = res05_lfc[order(res05_lfc$logFC),]
head(res05_lfc_ordered)
#res05ordered_lfc$symbol = mapIds(org.Dr.eg.db,keys = row.names(res05ordered_lfc),column = "SYMBOL",keytype = "ENSEMBL", multiVals="first")
#data for VennDiagram analysis
write.csv(res05_lfc_ordered,file="rps19morphant_vs_CtlDEG.csv")