read.bedix: Retrieve a subset of an indexed BED file.

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Using Rsamtools functions to manipulate tabix file, the indexed BED file is read and only regions defined by the desired subset are retrieved.

Usage

read.bedix(file, subset.reg = NULL, header = TRUE, as.is = TRUE,
  exact.match = FALSE)

Arguments

file	the name of the file which the data are to be read from. Should be compressed with |codebgzip and indexed by tabix algorithm.
subset.reg	a data.frame or GRanges object with the regions to subset from. If a data.frame, it must have columns named 'chr', 'start' and 'end'.
header	Should the first line be used as headers. Default is TRUE.
as.is	controls the conversion of columns. Default is TRUE, i.e. columns are converted into 'character', 'numeric', 'integer', etc. If FALSE, some columns might be converted into factors (e.g. 'character' columns).
exact.match	Should the input bins be exactly matched in the output file. If FALSE (default), overlapping bins in 'file' will also be returned.

Value

a data.frame with the retrieved BED information.

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.