filterCDS: Filter CDS by size

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Filter CDS by size

Description

Filter CDS by CDS size.

Usage

filterCDS(CDS, sizeCutoff = 100L)

Arguments

CDS	Output of preparedCDS
sizeCutoff	numeric(1). Cutoff size for CDS. If the size of CDS is less than the cutoff, it will be filtered out.

Value

A GRanges object with filtered CDS.

Examples

#library(GenomicFeatures)
library(BSgenome.Drerio.UCSC.danRer10)
#txdb <- makeTxDbFromGFF(system.file("extdata",
 #         "Danio_rerio.GRCz10.91.chr1.gtf.gz",
 #         package="ribosomeProfilingQC"),
 #         organism = "Danio rerio",
 #         chrominfo = seqinfo(Drerio)["chr1"],
 #         taxonomyId = 7955)
#CDS <- prepareCDS(txdb)
CDS <- readRDS(system.file("extdata", "CDS.rds",
                           package="ribosomeProfilingQC"))
filterCDS(CDS)

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