metagwa.files: Meta-analysis of a series of results from GWA scans

In MetABEL: Meta-Analysis of Genome-Wide SNP Association Results

Meta-analysis of a series of results from GWA scans

Description

Performes meta-analysis of results of multiple GWA studies stored in files.

Usage

metagwa.files(dir = ".", pops, extens, maf = 5, call = 0.95,
  phwe = 1e-08, precorrect = TRUE, correct.pooled = FALSE)

Arguments

dir	Path to directory containing files with GWA results
pops	A vector specifying study names, which make the first part of the file names
extens	Fixed extension to the file name
maf	Filter threshold for the absolute number/frequency of minor allele. If the parameter is < 1, this MAF threshold is used for filtering before meta-analysis; if this parameter is >1, n*MAF – absolute number of the minor allele copies – is used
call	Filter threshold for SNP call rate
phwe	Filter threshold for SNP P-value for HWE
precorrect	Should GC be applied to the original data before pooling
correct.pooled	Whether to apply Genomic Control correction to the study named "POOLED"

Details

The function looks for files named "POPSextens" in the directory "dir", reads them and pool consecutively using metagwa.tables function.

The source files should contain a number of variables, such as allelic coding, code for the effective allele, etc. Please refer to the formetascore function of GenABEL package for details.

When the file is not available for the first population, or there are non-unique population names, the function stops with an error message.

If there are no files corresponding to next populations, these are skipped in analysis with a warning message (see details in the description of returned values).

Value

Results are dumped to file named "POOLEDextens" in the directory "dir". Additionally, a list is returned with elements

analysed.pops

list of populations successfully analysed

Author(s)

Yurii Aulchenko

See Also

metagwa.tables

MetABEL documentation built on May 12, 2022, 3 p.m.