les (version 1.22.0)

export,Les-method: export

Description

Exports the results into files for interaction with other software. Estimated regions can be exported in 'bed' and 'gff' format, $Lambda$ in 'wig' format.

Usage

export(object, file, format="bed", chr, range, description = "Lambda",
strand=".", group="les", precision=4, ...)
"export"(object, file, format="bed", chr, range,
description = "Lambda", strand=".", group="les", precision=4, ...)

Arguments

object

Object of class 'Les' containing experimental data, as returned by 'estimate' or 'regions'.

file

Character string specifying the file path and name for export.

format

Character string with the export format (default: 'bed'). Possible values are 'bed' and 'gff' for export of the estimated regions and 'wig' for export of $Lambda$ for the probes. If set to 'bed' or 'gff' the method 'regions' has to be run beforehand. Partial matches are also possible. For details on the formats please see the 'Details' section.

chr

Character string specifying the chromosome from which results should be exported. This value must be set if exporting to 'wig' format, for other formats is optional. 'chr' must have exactly one match in the 'chr' argument specified in 'Les'.

range

Numeric vector specifying the range of probe positions which should be exported. If missing all probes of the chromosome will be exported. This value has only an effect if 'format' is set to 'wig'.

description

Character string with description for the exported track (default: 'Lambda'). This will be used as description by several programs and genome browsers.

strand

Character string with strand specification for 'gff' export (default: '.'). Possible values are '+', '-' or '.'.

group

Character string with group specifications of the resulting regions in 'gff' format (default: 'les').

precision

Integer specifying the number of digits $Lambda$ should be rounded to for export to 'wig' format (default: 4).

...

Further arguments passed to subsequent functions.

Details

This function is useful to export the estimated Lambda to external programs and genome browsers.

The 'bed', 'gff' and 'wig' format provide widely used standard formats and are compatible with most genome browsers and related software. For details about the file formats see http://genome.ucsc.edu/FAQ/FAQformat.html.

See Also

Package: les-package

Class: Les Methods and functions: Les estimate threshold regions ci chi2 export plot

Examples

## Not run: 
# data(spikeInStat)
# 
# x <- Les(pos, pval)
# x <- estimate(x, 200)
# x <- threshold(x)
# x <- regions(x)
# 
# export(x, file="test.bed")
# export(x, file="test.gff", format="gff")
# export(x, file="test.wig", format="wig", chr=0)
# ## End(Not run)