readGeneric: Read a tabular 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 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.

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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")

`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.

GRanges object

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)