adjStat {qgg}

Adjustment of marker summary statistics using clumping and thresholding

Description

Adjust marker summary statistics using linkage disequilibrium information from Glist.

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

Specify 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 correspond 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".

Details

Required input format for summary statistics:

stat can be a data.frame(rsids, chr, pos, ea, nea, eaf, b, seb, stat, p, n) (single trait)

stat can be a list(marker=(rsids, chr, pos, ea, nea, eaf), b, seb, stat, p, n) (multiple trait)

For details about the summary statistics format, see the main function description.

Author(s)

Peter Soerensen