get.baits: Read capture hybridization probe positions

Description

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

Usage

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

Arguments

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

Value

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

Details

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'.

Examples

Run this code

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)