simReads: Function to simulate paired end reads following given read...

In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description

This function generates path counts and bam files with simulated paired end reads according to given read start distribution, fragment length distribution and gene and variant expressions.

Usage

simReads(islandid, nSimReads, pis, rl, seed, writeBam, distrs, genomeDB,
repSims=FALSE, bamFile=NULL, stranded=FALSE, verbose=TRUE, chr=NULL, mc.cores=1)

Arguments

islandid	Island ID's from the genomeDB object to simulate reads
nSimReads	Named numeric vector with number of fragments to simulate in each island.
pis	Named numeric vector with relative expression of transcripts. Expressions add up to one for each island to simulate.
rl	Read length
seed	Seed of the random numbers generator
writeBam	Set to 1 to generate bam files with the simulated reads
distrs	Object of class 'readDistrs' with read start and fragment length distributions
genomeDB	Object of class 'annotatedGenome' with the genome to genererate reads from
repSims	Set to TRUE to return relative read starts and fragment lengths from the simulation
bamFile	Name of the bam file to write reads to. Must end with '.bam'
stranded	Set to TRUE to preserve gene strand when generating reads. The 'XS' tag will be added to reads in the bam file and the returned 'pc' object will be stranded
verbose	Set to TRUE to print progress
chr	Characters vector with chromosomes to simulate. Defaults to whole genome simulations.
mc.cores	Number of cores to use in function

Value

Nsim	Numerical vector with the number of reads simulated for each island.
pc	Object of class 'pathCounts' with simulated path counts
sims	Only if 'repSims' is set to TRUE. List with vectors of length 'n' with the following elements: -'varl': Length of variant for corresponding read -'st' Start of fragment relative to variant start (not in genomic coordinates) -len:Fragment length -'strand':Strand of gene for simulated read

Author(s)

Camille Stephan-Otto Attolini

Examples

data(hg19DB)
data(K562.r1l1)
distrs <- getDistrs(hg19DB,bam=K562.r1l1,readLength=75)

islandid <- c('10319','463')
txs <- unlist(lapply(hg19DB@transcripts[islandid], names))
pis <- vector(mode='numeric', length=length(txs))
npis <- sapply(hg19DB@transcripts[islandid],length)
pis[1:npis[1]] <- rep(1/npis[1],npis[1])
pis[-1:-npis[1]] <- rep(1/npis[2],npis[2])
names(pis) <- txs
nSimReads <- c(100, 100)
names(nSimReads) <- islandid

simpc <- simReads(islandid=islandid, nSimReads=nSimReads, pis=pis,
rl=75, repSims=TRUE, seed=1, writeBam=FALSE, distrs=distrs,genomeDB=hg19DB)

casper documentation built on Dec. 17, 2020, 2:01 a.m.