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qgg (version 1.1.1)

adjStat: LD adjustment of marker summary statistics

Description

Adjust marker summary statistics using linkage disequilibrium information from Glist

Required input format for summary statistics:

stat can be a data.frame(rsids, chr, pos, a1, a2, af, b, seb, stat, p, n) (single trait)

stat can be a list(marker=(rsids, chr, pos, a1, a2, af), b, seb, stat, p, n) (multiple trait)

Usage

adjStat(
  stat = NULL,
  Glist = NULL,
  chr = NULL,
  statistics = "b",
  r2 = 0.9,
  ldSets = NULL,
  threshold = 1,
  header = NULL,
  method = "pruning"
)

Arguments

stat

a data frame with marker summary statistics (see required format above)

Glist

list of information about genotype matrix stored on disk

chr

chromosome(s) being processed

statistics

specificy what type of statistics ("b" or "z") is being processed (default is "b")

r2

threshold used in clumping/pruning procedure (default is 0.9)

ldSets

list of marker sets - names corresponds to row names in stat

threshold

p-value threshold used in clumping procedure (default is 1)

header

character vector with column names to be excluded in the LD adjustment

method

method used in adjustment for linkage disequilibrium (default is "clumping")

Author

Peter Soerensen

Details

stat can be a data.frame(rsids, chr, pos, a1, a2, af, b, seb, stat, p, n) (single trait)

stat can be a list(marker=(rsids, chr, pos, a1, a2, af), b, seb, stat, p, n) (multiple trait)