createUCSCtrack: Turn beta values into a UCSC browser track

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Turn beta values into a UCSC browser track

Usage

createUCSCtrack(betas, output = NULL, platform = "HM450", refversion = "hg38")

Arguments

betas	a named numeric vector
output	output file name
platform	HM450, EPIC etc.
refversion	hg38, hg19 etc.

Value

when output is null, return a data.frame, otherwise NULL

Examples

betas.tissue <- sesameDataGet('HM450.1.TCGA.PAAD')$betas
## add output to create an actual file
df <- createUCSCtrack(betas.tissue)

## to convert to bigBed
## sort -k1,1 -k2,2n output.bed >output_sorted.bed
## bedToBigBed output_sorted.bed hg38.chrom output.bb

sesame documentation built on Nov. 15, 2020, 2:08 a.m.