pos2fastq: Convert read positions to fastq records

In ChIPsim: Simulation of ChIP-seq experiments

Description

Convert read positions for a single chromosome (both strands) into read sequences + qualities and write them to file

Usage

pos2fastq(readPos, names, quality, sequence, qualityFun, errorFun, 
	readLen = 36, file, 
	qualityType = c("Illumina", "Sanger", "Solexa"), ...)

Arguments

readPos	A list of two numeric vectors (one per strand)
names	List of names to use for reads in fastq file. Has to be of same shape as name.
quality	Passed on as argument to qualityFun.
sequence	Reference sequence (a DNAString object).
qualityFun	Function to generate quality scores.
errorFun	Function to introduce sequencing errors.
readLen	Read length to generate.
file	Output file (either file name or connection).
qualityType	Encoding to use for read quality scores.
...	Further arguments (see Details).

Details

Arguments passed as part of ... will be passed on to qualityFun, except an argument called prob which is passed on to errorFun instead if present.

Value

Invisibly returns the number of records that were written.

Author(s)

Peter Humburg

See Also

See readError for a possible choice of errorFun and readQualitySample for a simple qualityFun.

Examples

set.seed(1)

## a function to generate random read qualities (in Sanger format)
randomQuality <- function(read, ...){
	paste(sample(unlist(strsplit(rawToChar(as.raw(33:126)),"")), 
		length(read), replace = TRUE), collapse="")
} 

## generate a reference sequence
chromosome <- DNAString(paste(sample(c("A", "C", "G", "T"), 
	1e5, replace = TRUE), collapse = ""))

## and a few read positions
reads <- list(sample(100:9900, 5), sample(100:9900, 5))
names <- list(paste("read", 1:5, sep="_"), paste("read", 6:10, sep="_"))

## convert to fastq format
pos2fastq(reads, names, sequence=chromosome, qualityFun=randomQuality, 
	errorFun=readError, file="")

ChIPsim documentation built on Nov. 8, 2020, 8:09 p.m.