methSeg2bed: Export segments to BED files

In al2na/methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

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,
  filename,
  trackLine = "track name='meth segments' description='meth segments' itemRgb=On",
  colramp = colorRamp(c("gray", "green", "darkgreen"))
)

Arguments

segments	GRanges object with segment classification and information. This should be the result of methSeg function
filename	name of the output data
trackLine	UCSC browser trackline
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

al2na/methylKit documentation built on Nov. 30, 2024, 5:44 p.m.