findAndAnnoPAs: findAndAnnoPAs

In XHWUlab/PolyAtailor: a toolkit for analyzing poly(A) tail length dynamics from xxx RNA-seq data

Description

Find and annotate PA sites.

Usage

findAndAnnoPAs(
  chrinfo,
  bamfile,
  resultpath,
  bsgenome,
  gffFile,
  sample,
  mergePAs,
  d
)

Arguments

chrinfo	The path of chrinfo file.
bamfile	The path of bam file.
resultpath	The path of result file.
bsgenome	BSgenome package for your species, please refer to movAPA package for details.
gffFile	Genome annotation stored in a GFF/GTF file or a TXDB R object can be used for annotating PACs. Please refer to movAPA for details.
sample	The sample name.
mergePAs	TRUE/FALSE. If TRUE, then will mergePACds groups nearby PACs from single/multiple PACdataset objects.
d	distance to group nearby PACds, default is 24 nt.

Value

The function returns data in PACds format with the annotation information for all PA sites. In addition, we will also generate a "pac_data.txt" file to store the PA annotation table under the result path you specified, and a "pac_data.coldata.txt" file to store the additional comment information.And an "ACTGpdf.PDF" file, which holds a legend of the base composition around the PACs, has two images representing the base composition of the plus and minus chains.

See Also

Other poly(A) sites detection functions: findPAs()

Examples

library(movAPA)
# Deciphering gff files
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
# Deciphering genome files
library("BSgenome.Mmusculus.UCSC.mm10")
bsgenome = BSgenome.Mmusculus.UCSC.mm10
bamfilepath = system.file("extdata", "./GV_algin/PAIso-GV1.sorted.bam",
package = "PolyAtailor", mustWork = TRUE)
chrinfopath = system.file("extdata", "./GV_algin/chrinfo.txt", package =
"PolyAtailor", mustWork = TRUE)
resultpath = "./"
# Annotated PA site
PAs <- findAndAnnoPAs(bamfile=bamfilepath,chrinfo=chrinfopath,resultpath=resultpath,bsgenome=bsgenome,gffFile = TxDb.Mmusculus.UCSC.mm10.knownGene,sample="GV1",mergePAs=T,d=24)

XHWUlab/PolyAtailor documentation built on Dec. 28, 2021, 12:13 a.m.