comp.ss.bim: Compare summary statistics and PLINK .bim data.frames

In tshmak/lassosum: LASSO with summary statistics and a reference panel

Description

Compare summary statistics and PLINK .bim data.frames

Usage

comp.ss.bim(ss.df, bim.df, exclude.ambiguous = F)

Arguments

ss.df	A data.frame of summary statistics
bim.df	a data.frame from A PLINK .bim file
exclude.ambiguous	should ambiguous SNPs (i.e. A/T or G/C) be excluded

Details

Both ss.df and bim.df must be data.frames with exactly three columns in this order: (1) SNP ids, (2) reference allele, (3) alternative allele

Value

A list with 3 vectors

ss.order	the order the SNPs in the summary statistics must be rearranged in
bim.extract	the SNPs to be extracted from the PLINK bfile, i.e. that are in the summary statistics data.frame
rev	A vector of 1 and -1 to facilitate the flipping SNPs effects for SNPs whose reference and alternative alleles are reversely coded between the two data.frames

tshmak/lassosum documentation built on Sept. 24, 2020, 9:41 a.m.