Usage
readGeneric(file, chr = 1, start = 2, end = 3, strand = NULL,
meta.cols = NULL, keep.all.metadata = FALSE, zero.based = FALSE,
remove.unusual = FALSE, header = FALSE, skip = 0, sep = "\t")
Arguments
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).
chr
number of the column that has chromsomes information in the table (Def:1)
start
number of the column that has start coordinates in the table (Def:2)
end
number of the column that has end coordinates in the table (Def:3)
strand
number of the column that has strand information, only -/+
is accepted (Default:NULL)
meta.cols
named list that maps column numbers to
meta data columns.
e.g. list(name=5, score=10), which means 5th column will be
named "name", and 10th column will be named "score" and their
contents will be a part of the returned GRanges object.
If header = TRUE, meta.cols parameter will over-write the
column names given by the header line of the data frame.
keep.all.metadata
logical determining if the extra columns (
the ones that are not designated by chr,start,end,strand and meta.cols
arguments )
should be kept or not. (Default:FALSE)
zero.based
a boolean which tells whether the ranges in
the bed file are 0 or 1 base encoded. (Default: FALSE)
remove.unusual
if TRUE(default) remove the chromosomes with unsual
names, such as chrX_random (Default:FALSE)
header
whether the original file contains a header line
which designates the column names. If TRUE header will be used to
construct column names. These names can be over written by meta.cols argument.
skip
number of lines to skip. If there is a header line(s) you do not
wish to include you can use skip argument to skip that line.
sep
a single character which designates the separator in the file.
The default value is tab.