normByRUVs {ribosomeProfilingQC} | R Documentation |
Normalization by RUVSeq:RUVs methods
normByRUVs(counts, RPFgroup, mRNAgroup = RPFgroup, k = 1)
counts |
Output of countReads |
RPFgroup, mRNAgroup |
Groups for RPF and mRNA files |
k |
The number of factor of unwanted variation to be estimated from the data. See RUVs |
Normalized counts list
## Not run: ##waiting for EDASeq fix the issue. path <- system.file("extdata", package="ribosomeProfilingQC") #RPFs <- dir(path, "RPF.*?.[12].bam$", full.names=TRUE) #RNAs <- dir(path, "mRNA.*?.[12].bam$", full.names=TRUE) #gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz") #cnts <- countReads(RPFs, RNAs, gtf, level="gene") cnts <- readRDS(file.path(path, "cnts.rds")) gp <- c("KD1", "KD1", "WT", "WT") norm <- normByRUVs(cnts, gp, gp) ## End(Not run)