library(Rsamtools)
library(GenomicFeatures)
sampleTable = read.table("bamfiles.txt")
dirActualData = paste(getwd(),"/",sep="")
fls = paste(dirActualData,sampleTable[,1],sep="")
bamLst = BamFileList(fls, index=character(),yieldSize=100000,obeyQname=TRUE)
gtfFile = "../Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
txdb = makeTxDbFromGFF(gtfFile, format="gtf")
genes = exonsBy(txdb, by="gene")
library(GenomicAlignments)
PRJNA297664 = summarizeOverlaps(features = genes, read=bamLst,
mode="Union",
singleEnd=TRUE, ## No son lecturas apareadas
ignore.strand=TRUE,
fragments=FALSE)
SampleName = c("GSM1900735","GSM1900737","GSM1900739","GSM1900736",
"GSM1900738","GSM1900740")
Run = c("SRR2549634","SRR2549636","SRR2549638","SRR2549635",
"SRR2549637","SRR2549639")
treatment = c(0,0,1,0,1,1)
treatment = factor(treatment,levels=0:1,labels=c("Wild","SEC66 deletion"))
replication = c(1,3,2,2,1,3)
colData(PRJNA297664) = DataFrame(SampleName,Run,treatment,replication)