get.baits: Read capture hybridization probe positions
In hummelma/TEQC: Quality control for target capture experiments

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

Reads a file containing positions and sequences of the capture hybridization probes and creates a RangedData object.

1	get.baits(baitsfile, chrcol = 1, startcol = 2, endcol = 3, seqcol = 4, zerobased = TRUE, sep = "\t", header = TRUE, ...)

`baitsfile`	name of file giving the positions and sequences of each hybridization probe ("bait")
`chrcol`	in which column in `baitsfile` 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 baits
`endcol`	in which column there are the end positions of the baits
`seqcol`	in which column there are the sequences of the baits
`zerobased`	if `TRUE`, start coordinates in `baitsfile` 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 `baitsfile`.
`sep`	column separator character, defaults to tabs
`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`

The baitsfile containing positions and sequences of hybridization probes has to be created beforehand, in many cases manually. (The function was made like this in order to keep things as general and platform independent as possible.) E.g. with baits designed by Agilent's eArray tool, the baitsfile can be created by merging the files '..._D_BED_...bed' and '..._D_DNAFront_BCBottom_...txt'.

A RangedData table holding the hybridization probe ("bait") positions and sequences. Overlapping or adjacent baits are not collapsed.

Manuela Hummel m.hummel@dkfz.de

get.reads, get.targets

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exptPath <- system.file("extdata", package="TEQC")
baitsfile <- file.path(exptPath, "ExampleSet_Baits.txt")
baits <- get.baits(baitsfile, chrcol=3, startcol=4, endcol=5, seqcol=2)