get.reads {TEQC} | R Documentation |
Reads a bedfile containing positions of sequenced read aligned to a reference genome
and creates a RangedData
object.
get.reads(readsfile, filetype = c("bed", "bam"), chrcol = 1, startcol = 2, endcol = 3, idcol, zerobased = TRUE, sep = "\t", skip = 1, header = FALSE, ...)
readsfile |
name of bedfile giving the positions of aligned reads |
#!!
filetype |
Input file type. If |
# !!
chrcol |
In which column in the reads bedfile there is the chromosome information
(chromosome information in the file should be in string format, e.g. "chrX").
Ignored if |
startcol |
In which column there are the starting positions of the reads.
Ignored if |
endcol |
In which column there are the end positions of the reads.
Ignored if |
idcol |
In which column there are read identifiers. For single-end data it is optionally.
For paired-end data it is required for some functionalities. The two reads of one pair need to have the same ID.
Ignored if |
zerobased |
if |
sep |
Column separator character, defaults to tabs. Ignored if |
skip |
Number of lines of the bedfile to skip before beginning to read data; defaults to 1.
Ignored if |
header |
A logical value indicating whether the file contains the names of the variables as its first line;
defaults to FALSE. Ignored if |
... |
Further arguments passed to |
A RangedData
table holding the read positions
Manuela Hummel m.hummel@dkfz.de
exptPath <- system.file("extdata", package="TEQC") readsfile <- file.path(exptPath, "ExampleSet_Reads.bed") reads <- get.reads(readsfile, idcol=4, skip=0)