methylKit (version 0.99.2)

methSeg2bed: Export segments to BED files

Description

The segments are color coded based on their score (methylation or differential methylation value). They are named by segment group (components in mixture modeling) and the score in the BED file is obtained from 'seg.mean' column of segments object.

Usage

methSeg2bed(segments,
  trackLine = "track name='meth segments' description='meth segments' itemRgb=On",
  filename = "data/H1.chr21.chr22.trial.seg.bed",
  colramp = colorRamp(c("gray", "green", "darkgreen")))

Arguments

segments

GRanges object with segment classification and information. This should be the result of methSeg function

trackLine

UCSC browser trackline

filename

name of the output data

colramp

color scale to be used in the BED display defaults to gray,green, darkgreen scale.

Value

A BED files with the segmented data which can be visualized in the UCSC browser

See Also

methSeg