gwaa.to.bed: Create a BED file with GWAS p-values in a region

In cgmisc-team/cgmisc: Various functions useful in computational genetics, e.g. in GWAS

Create a BED file with GWAS p-values in a region

Description

Returns a file containing GWAS p-values for a region in bed format. It can be further used as UCSC Genome Browser custom track.

Usage

gwaa.to.bed(chr, range, gwas, fname = "output.bed")

Arguments

chr	chromosome to be considered
range	a vector of genomic ranges
gwas	a scan.gwaa-class object produced by GenABEL
fname	name of the output file. By default: output.bed

Value

a bed file with -log10 of corrected p-value ("Pc1df")

Author(s)

Marcin Kierczak <[e-mail]>

Examples

## Not run: 
 chr <- 36
 range <- c(14e6,24e6)
 gwas <- data.qc1
 gwas.region.bed(chr, range, gwas, fname="my_output.bed")
 
## End(Not run)

cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.