casper (version 2.6.0)

simReads: Function to simulate paired end reads following given read start and fragment length distributions and gene and variant expressions.

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

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)