loadLd: loadLd

In VSE: Variant Set Enrichment

Description

This function will load a raggr output csv or user defined bed file to GRanges object. It is recommended to generate a LD file using http://raggr.usc.edu. If you prefer to use other softwares to calculate LD SNPs (e.g., plink), please format the output to bed files. Please make sure that you use a cutoff of 0.8 for r2 value.

Usage

loadLd(data, type)

Arguments

data	An input file. Must be a raggr generated csv file or a bed file. If a bed file, it must contain at least five columns: chr, start, end, LD_snp_id, tag_snp_id.
type	The type of input file. Must be "bed" or "raggr".

Examples

ld<-loadLd(file.path(system.file("extdata", "ld_BCa_raggr.csv", package="VSE")), type="raggr")

VSE documentation built on May 2, 2019, 4 p.m.