MetABEL (version 0.2-0)

metagwa.files: 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"

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

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).

See Also

metagwa.tables