readsEndPlot: Plot start/stop windows

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Plot start/stop windows

Description

Plot the reads shifted from start/stop position of CDS.

Usage

readsEndPlot(
  bamfile,
  CDS,
  toStartCodon = TRUE,
  fiveEnd = TRUE,
  shift = 0,
  window = c(-29, 30),
  readLen = 25:30,
  ignore.seqlevelsStyle = FALSE
)

Arguments

bamfile	A BamFile object.
CDS	Output of prepareCDS
toStartCodon	What to search: start or end codon
fiveEnd	Search from five or three ends of the reads.
shift	number(1). Search from 5' end or 3' end of given number. if fiveEnd set to false, please set the shift as a negative number.
window	The window of CDS region to plot
readLen	The reads length used to plot
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.

Value

The invisible list with counts numbers and reads in GRanges.

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"))
re <- readsEndPlot(bamfile, CDS, toStartCodon=TRUE)
readsEndPlot(re$reads, CDS, toStartCodon=TRUE, fiveEnd=FALSE)
#re <- readsEndPlot(bamfile, CDS, toStartCodon=FALSE)
#readsEndPlot(re$reads, CDS, toStartCodon=FALSE, fiveEnd=FALSE)
readsEndPlot(bamfile, CDS, shift=13)
#readsEndPlot(bamfile, CDS, fiveEnd=FALSE, shift=-16)

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.