R: Meta-analysis of seriens of results GWA scans

metagwa.files {MetABEL}R Documentation

Meta-analysis of seriens of results 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 = F)

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

Th 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 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


[Package MetABEL version 0.0-3 Index]