get.targets: Read capture target positions
In TEQC: Quality control for target capture experiments

Description Usage Arguments Value Note Author(s) See Also Examples

Reads a bedfile containing positions of the capture targets and creates a RangedData object.

1	get.targets(targetsfile, chrcol = 1, startcol = 2, endcol = 3, zerobased = TRUE, sep = "\t", skip = 1, header = FALSE, ...)

`targetsfile`	name of bedfile giving the positions of each target region
`chrcol`	in which column in the targets bedfile there is the chromosome information (chromosome information in the file should be in string format, e.g. "chrX")
`startcol`	in which column there are the starting positions of the targeted regions
`endcol`	in which column there are the end positions of the targeted regions
`zerobased`	if `TRUE`, start coordinates in `targetsfile` 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 `targetsfile`.
`sep`	column separator character, defaults to tabs
`skip`	number of lines of the bedfile to skip before beginning to read data; defaults to 1
`header`	a logical value indicating whether the file contains the names of the variables as its first line; defaults to FALSE
`...`	further arguments passed to `read.delim`

A RangedData table holding the target region positions. Note that overlapping or adjacent regions are collapsed to one region.

Since overlapping regions are collapsed, the input bedfile can also contain positions of the (in most cases overlapping) hybridization probes used for the target capture.

Manuela Hummel m.hummel@dkfz.de

get.reads

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exptPath <- system.file("extdata", package="TEQC")
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

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[1] "read 50 (non-overlapping) target regions"