ldRACER: Calculating Linkage Disequilibrium Information for Regional...
In oliviasabik/mirrorplot: Regional Association Comparer

Description Usage Arguments Examples

View source: R/ldRACER.R

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().

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

`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

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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"))