merge_sumstats: Merge summary statistics into a single input data frame

In LizaDarrous/lhcMR: Latent Heritable Confounder - Mendelian Randomisation

Merge summary statistics into a single input data frame

Description

Merge summary statistics into a single input data frame

Usage

merge_sumstats(
  input.files,
  trait.names,
  LD.filepath,
  rho.filepath,
  mafT = 0.005,
  infoT = 0.99
)

Arguments

input.files	list of data frames, where each data frame contains the summary statistics of a trait to use in the order of Exposure - Outcome
trait.names	Vector containing the trait names in the order they're found in 'input files'
mafT	Minor allele frequency threshold of selection, to be used if a MAF column is found in the summary statistics file. Default value = 0.005
infoT	SNP imputation quality threshold, to be used if an INFO column is found in the summary statistics file. Default value = 0.99
LD.file	LD scores file, either obtained from Alkes group (1000G) or the one provided in the github (UK10K)
rho.file	Genotyped SNP-specific (local) LD scores

Value

Returns a data frame where the summary statistics file, the LD file, and the SNP-specific LD file are merged

LizaDarrous/lhcMR documentation built on March 24, 2024, 10:28 p.m.