addDummyProb: Create a dummy GRanges object as a placeholder in case nbh_em...

In RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Description

This function is used to generate a place holder in cases the EM fails to converge on a chromosome due to too few number of reads mapped to that chromosome. This is an internal function not expected to be directly called by the user.

Usage

addDummyProb(alignGR, K = 2, randomProb = FALSE, runViterbi = FALSE, ...)

Arguments

alignGR	GRanges object derived from RIP-seq alignment inputs.
K	Number of hidden states (Default: 2).
randomProb	A binary value to indicate whether to use random probability as a place holder to present posterior probabilities. If set FALSE, (by default), equal probability is used for all states.
runViterbi	A binary value to indicate whether to generate place holder for the Viterbi state sequence (Default: FALSE).
...	Additional arguments expected to contain the bin size used for computing the bin counts in binCount function, and any other extra arguments are ignored.

Details

A priviate function to fall back in case HMM fails to converge mostly due to too many zero counts in the input vector. When that occurs, a GRanges place holder object needs to be returned to keep consistent with the remaining GRanges for each chromosome. Thus, all information slot will be generated as place holder to properly create the GRangesList for the predictions on all chromosomes (each as an GRanges item in the list).

Value

GRanges

A GRanges object containing the read count (in the defined bin size), alpha, beta, TRANS dummy values for the HMM

Author(s)

Yue Li

See Also

mainSeekSingleChrom

Examples

# Retrieve system files
extdata.dir <- system.file("extdata", package="RIPSeeker") 

bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

bamFiles <- grep("PRC2", bamFiles, value=TRUE)

alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")

alignGR <- as(alignGal, "GRanges")

alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))

x <- addDummyProb(alignGRList$chrX, binSize=10000)

x

RIPSeeker documentation built on Oct. 31, 2019, 7:29 a.m.