estimatePsite: Estimate P site position

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Estimate P site position

Description

Estimate P site position from a subset reads.

Usage

estimatePsite(
  bamfile,
  CDS,
  genome,
  anchor = "5end",
  readLen = c(25:30),
  ignore.seqlevelsStyle = FALSE
)

Arguments

bamfile	A BamFile object.
CDS	Output of prepareCDS
genome	A BSgenome object.
anchor	5end or 3end. Default is 5end.
readLen	The reads length used to estimate.
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.

Value

A best P site position.

References

1: Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. 2014 May 2;33(9):981-93. doi: 10.1002/embj.201488411. Epub 2014 Apr 4. PubMed PMID: 24705786; PubMed Central PMCID: PMC4193932.

Examples

library(Rsamtools)
bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                           package="ribosomeProfilingQC")
yieldSize <- 10000000
bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
#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"))
estimatePsite(bamfile, CDS, Drerio)

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