TEQC (version 3.12.0)

get.reads: Read genomic positions of sequencing data

Description

Reads a bedfile containing positions of sequenced read aligned to a reference genome and creates a RangedData object.

Usage

get.reads(readsfile, filetype = c("bed", "bam"), chrcol = 1, startcol = 2, endcol = 3, idcol, zerobased = TRUE, sep = "\t", skip = 1, header = FALSE, ...)

Arguments

readsfile

name of bedfile giving the positions of aligned reads

filetype

Input file type. If "bam", the .bam file is read using scanBam, where flag option isUnmappedQuery=FALSE is used. Defaults to "bed"

chrcol

In which column in the reads bedfile there is the chromosome information (chromosome information in the file should be in string format, e.g. "chrX"). Ignored if filetype = "bam".

startcol

In which column there are the starting positions of the reads. Ignored if filetype = "bam".

endcol

In which column there are the end positions of the reads. Ignored if filetype = "bam".

idcol

In which column there are read identifiers. For single-end data it is optionally. For paired-end data it is required for some functionalities. The two reads of one pair need to have the same ID. Ignored if filetype = "bam" (the ID column is automatically included then). If read IDs include "#0/1" and "#0/2" in the end (indicating read 1 and read 2 of a pair), those characters will be removed from the IDs.

zerobased

if TRUE, start coordinates in readsfile are assumed to be 0-based and are then converted to 1-based system by adding 1. If FALSE, coordinates are not shifted. In this case they should already be 1-based in readsfile. Ignored if filetype = "bam", since scanBam converts 0-based to 1-based coordinates.

sep

Column separator character, defaults to tabs. Ignored if filetype = "bam".

skip

Number of lines of the bedfile to skip before beginning to read data; defaults to 1. Ignored if filetype = "bam".

header

A logical value indicating whether the file contains the names of the variables as its first line; defaults to FALSE. Ignored if filetype = "bam".

...

Further arguments passed to read.delim. Ignored if filetype = "bam".

Value

RangedData table holding the read positions

See Also

get.targets

Examples

exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)