ldRACER: Calculating Linkage Disequilibrium Information for Regional...

In oliviasabik/mirrorplot: Regional Association Comparer

Calculating Linkage Disequilibrium Information for Regional Association ComparER

Description

This group of functions allows you to creat a plot of -log10(P-values) of an association study by their genomic position, for example, the results of a GWAS or eQTL study. This function takes the rsID of a reference SNP and calculates LD for all other SNPs in the dataset using the 1000 Genomes Phase III Data. This function takes a lead SNP, or finds the most significantly associated SNP in the input data set and use it as the lead SNP (auto_snp = TRUE). The input of the function should already have been formatted using formatRACER().

Usage

ldRACER(assoc_data, rs_col, pops, lead_snp = NULL, auto_snp = FALSE)

Arguments

assoc_data	required. A dataframe produced by by formatRACER()
rs_col	required. numeric or character. index of column or name of column containing rsID numbers for SNPs
pops	required. Populations used to calculate LD. Options can be found at the LD Link website.
lead_snp	required, unless auto_snp = TRUE. Required if ldby = "1000genomes". snp used to calculate LD
auto_snp	optional. default = FALSE, can be set to TRUE to calculate LD using the highest LOG10P SNP as the reference

Examples

data(mark3_bmd_gwas)
mark3_bmd_gwas_f = formatRACER(assoc_data = mark3_bmd_gwas, chr_col = 3, pos_col = 4, p_col = 11)
head(ldRACER(assoc_data = mark3_bmd_gwas_f, rs_col = 5, pops = c("EUR"), lead_snp = "rs11623869"))

oliviasabik/mirrorplot documentation built on Dec. 20, 2024, 11:11 p.m.