CPsites: predict the cleavage and polyadenylation(CP) site

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Description

predict the alternative cleavage and polyadenylation (CP or APA) site.

Usage

    CPsites(coverage, groupList=NULL, genome, utr3, 
        window_size=100, search_point_START=50, search_point_END=NA, 
        cutStart=window_size, cutEnd=0, adjust_distal_polyA_end=TRUE, 
        coverage_threshold=5, long_coverage_threshold=2, 
        background=c("same_as_long_coverage_threshold", 
                     "1K", "5K", "10K", "50K"),
        txdb=NA,
        PolyA_PWM=NA, classifier=NA, classifier_cutoff=.8, step=1, 
        two_way=FALSE,
        shift_range=window_size,
        BPPARAM=NULL, tmpfolder=NULL, silence=TRUE)

Arguments

coverage	coverage for each sample, output of coverageFromBedGraph
groupList	group list of tag names
genome	an object of BSgenome
utr3	output of utr3Annotation
window_size	window size for noval distal position searching and adjusted polyA searching, default: 100
search_point_START	start point for searching
search_point_END	end point for searching
cutStart	how many nucleotides should be removed from the start before search, 0.1 means 10 percent, 25 means cut first 25.
cutEnd	how many nucleotides should be removed from the end before search, 0.1 means 10 percent.
adjust_distal_polyA_end	If true, adjust distal polyA end by cleanUpdTSeq
coverage_threshold	cutoff coverage threshold for first 100 nucleotides. If the coverage of first 100 nucleotides is lower than coverage_threshold, that transcript will be dropped.
long_coverage_threshold	cutoff threshold for coverage in the region of long form. If the coverage in the region of long form is less than long_coverage_threshold, that transcript will be dropped.
background	the range for calculating cutoff threshold of local background
txdb	an object of TxDb
PolyA_PWM	Position Weight Matrix of polyA
classifier	An object of class "PASclassifier"
classifier_cutoff	This is the cutoff used to assign whether a putative pA is true or false. This can be any floating point number between 0 and 1. For example, classifier_cutoff = 0.5 will assign an putative pA site with prob.1 > 0.5 to the True class (1), and any putative pA site with prob.1 <= 0.5 as False (0).
step	adjust step, default 1, means adjust by each base by cleanUpdTSeq.
two_way	Search the proximal site from both direction or not.
shift_range	the shift range for polyA site searching
BPPARAM	An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to bplapply.
tmpfolder	temp folder could save and reload the analysis data for resume analysis.
silence	report progress or not. default not report.

Value

return an object of GRanges contain the estimated CP sites.

Author(s)

Jianhong Ou

References

ref: Cheung MS, Down TA, Latorre I, Ahringer J. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res. 2011 Aug;39(15):e103. doi: 10.1093/nar/gkr425. Epub 2011 Jun 6. PubMed PMID: 21646344; PubMed Central PMCID: PMC3159482.

mappability could be calculated by [GEM](http://algorithms.cnag.cat/wiki/Man:gem-mappability)

ref: Derrien T, Estelle J, Marco Sola S, Knowles DG, Raineri E, Guigo R, Ribeca P. Fast computation and applications of genome mappability. PLoS One. 2012;7(1):e30377. doi: 10.1371/journal.pone.0030377. Epub 2012 Jan 19. PubMed PMID: 22276185; PubMed Central PMCID: PMC3261895.

Examples

    if(interactive()){
        library(BSgenome.Mmusculus.UCSC.mm10)
        path <- file.path(find.package("InPAS"), "extdata")
        bedgraphs <- file.path(path, "Baf3.extract.bedgraph")
        data(utr3.mm10)
        tags <- "Baf3"
        genome <- BSgenome.Mmusculus.UCSC.mm10
        coverage <- 
            coverageFromBedGraph(bedgraphs, tags, genome, hugeData=FALSE)
        CP <- CPsites(coverage=coverage, gp1=tags, gp2=NULL, genome=genome, 
            utr3=utr3.mm10, coverage_threshold=5, long_coverage_threshold=5)
    }

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.