matchpos: Function to match a set of variants to a reference by...

In SeojinHwang/scadsum: nonconvex penalty with summary statistics and a reference panel

Function to match a set of variants to a reference by chromosome and/or position and/or SNP/rsIDs

Description

Function to match a set of variants to a reference by chromosome and/or position and/or SNP/rsIDs

Usage

matchpos(
  tomatch,
  ref.df,
  auto.detect.tomatch = T,
  auto.detect.ref = T,
  chr = "",
  ref.chr = "",
  pos = "",
  ref.pos = "",
  snp = "",
  ref.snp = "",
  ref = "",
  ref.ref = "",
  alt = "",
  ref.alt = "",
  exclude.ambiguous = F,
  silent = F,
  rm.duplicates = F
)

Arguments

tomatch	A data.frame or data.table
ref.df	A data.frame or data.table
rm.dumplicates	Remove SNPs with more than one match

Details

If REF/ALT alleles available, will also check them for reverse coding. Specify the exclude.ambiguous option for possible sense/antisense ambiguity.

Value

matched postions of SNPs

SeojinHwang/scadsum documentation built on June 30, 2023, 10:52 p.m.