get.reads: Read genomic positions of sequencing data
In TEQC: Quality control for target capture experiments

Description Usage Arguments Value Author(s) See Also Examples

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

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

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 options isUnmappedQuery=FALSE and isSecondaryAlignment=FALSE are 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"`.

A RangedData table holding the read positions

Manuela Hummel m.hummel@dkfz.de

get.targets

1
2
3

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

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

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The following objects are masked from 'package:base':

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    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
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    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
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Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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Loading required package: hwriter
[1] "read 19546 sequenced reads"