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Look for overlapped variants between SummarySets in the DataSet and Resize

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

Look for overlapped variants between SummarySets in the DataSet and Resize

Usage

overlapVariants(dataset, action)

# S4 method for DataSet
overlapVariants(dataset, action)

Arguments

dataset

The gwasglue2 DataSet object

action

Level of strictness in dealing with SNPs during harmonisation.

  • 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 resized