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Harmonise the alleles and effects between two summary sets

Source: R/harmonise_method.R
harmoniseData-methods.Rd

Harmonise the alleles and effects between two summary sets

Usage

harmoniseData(dataset, tolerance, action)

# S4 method for DataSet
harmoniseData(dataset, tolerance, action)

Arguments

dataset

The gwasglue2 DataSet object

tolerance

Tolerance value.

action

Level of strictness in dealing with SNPs.

  • action = 1: Assume all alleles are coded on the forward strand, i.e. do not attempt to flip alleles

  • action = 2: Try to infer positive strand alleles, using allele frequencies for palindromes (default, conservative);

  • action = 3: Correct strand for non-palindromic SNPs, and drop all palindromic SNPs from the analysis (more conservative).

Value

The gwasglue2 DataSet object harmonised