readBed

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 <code>.gz</code>, <code>.bz2</code>, <code>.xz</code>, or <code>.zip</code>
            and/or start with <code>http://</code> or <code>ftp://</code>. If the file is not
            compressed it can also start with <code>https://</code> or <code>ftps://</code>.

file

the number of track lines to skip, "auto" to detect them
                  automatically or FALSE(default) if the bed file doesn't
                  have track lines

track.line

if TRUE remove the chromosomes with unsual
names, such as chrX_random (Default:FALSE)

remove.unusual

a boolean which tells whether the ranges in
       the bed file are 0 or 1 base encoded. (Default: TRUE)

zero.based

The function reads a BED file that contains location and other information
on genomic features and returns a <code><a href="/link/GRanges?package=genomation&version=1.4.2" rd-options="" data-mini-rdoc="genomation::GRanges">GRanges</a></code> 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.

A package for summary and annotation of genomic intervals. Users can visualize and 
	quantify genomic intervals over pre-defined functional regions, such as promoters, exons, 
	introns, etc. The genomic intervals represent regions with a defined chromosome position,
	which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, 
	methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal 
	information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Altuna Akalin

genomation

Summary, annotation and visualization of genomic data

readBed function

The function reads a BED file that contains location and other information
on genomic features and returns a <code><a href="GRanges" rd-options="">GRanges</a></code> 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.

readBed: Read a BED file and convert it to GRanges.

Description

Usage

Arguments

Value

Examples