createUCSCtrack: Turn beta values into a UCSC browser track
In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

createUCSCtrack

R Documentation

Turn beta values into a UCSC browser track

Description

Turn beta values into a UCSC browser track

Usage

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

Arguments

`betas`	a named numeric vector
`output`	output file name
`platform`	HM450, EPIC etc.
`genome`	hg38, mm10, ..., will infer if not given. For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., genome = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.

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

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.