readGeneric: Read a tabular file and convert it to GRanges.

Description Usage Arguments Value Examples

View source: R/readData.R

Description

The function reads a tabular text file that contains location and other information on genomic features and returns a GRanges object. The minimal information that the file has to have is chromosome, start and end columns. Strand information is not compulsory.

Usage

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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.

Value

GRanges object

Examples

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my.file=system.file("extdata","chr21.refseq.hg19.bed",package="genomation")
refseq = readGeneric(my.file,chr=1,start=2,end=3,strand=NULL,
                      meta.cols=list(score=5,name=4),
                      keep.all.metadata=FALSE, zero.based=TRUE)
head(refseq)

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.