normByRUVs: Normalization by RUVSeq

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Normalization by RUVSeq

Description

Normalization by RUVSeq:RUVs methods

Usage

normByRUVs(counts, RPFgroup, mRNAgroup = RPFgroup, k = 1)

Arguments

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

Value

Normalized counts list

Examples

## 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)

jianhong/ribosomeProfilingQC documentation built on April 15, 2024, 7:10 p.m.