readBed: Read a BED file and convert it to GRanges.
In BIMSBbioinfo/genomation: Summary, annotation and visualization of genomic data

Description Usage Arguments Value Examples

The function reads a BED file that contains location and other information on genomic features and returns a GRanges object. The minimal information that the BED file has to have is chromosome, start and end columns. it can handle all BED formats up to 12 columns.

1 2	readBed(file, track.line = FALSE, remove.unusual = FALSE, zero.based = TRUE)

`file`	location of the file, a character string such as: "/home/user/my.bed" or the input itself as a string (containing at least one \n). The file can end in `.gz`, `.bz2`, `.xz`, or `.zip` and/or start with `http://` or `ftp://`. If the file is not compressed it can also start with `https://` or `ftps://`.
`track.line`	the number of track lines to skip, "auto" to detect them automatically or FALSE(default) if the bed file doesn't have track lines
`remove.unusual`	if TRUE remove the chromosomes with unsual names, such as chrX_random (Default:FALSE)
`zero.based`	a boolean which tells whether the ranges in the bed file are 0 or 1 base encoded. (Default: TRUE)

GRanges object

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my.file=system.file("extdata","chr21.refseq.hg19.bed",package="genomation")
refseq = readBed(my.file,track.line=FALSE,remove.unusual=FALSE)
head(refseq)