initFiles: Initialize files for enrichment analysis
In snpEnrichment: SNPs Enrichment Analysis

Description Usage Arguments Value Author(s) See Also Examples

initFiles create several files needed to run readEnrichment. ".frq" and ".signal" are created with PLINK. LD computation can be run with writeLD or with PLINK.

1	initFiles(pattern = "Chrom", snpInfoDir, signalFile, mc.cores = 1)

`pattern`	[character]: character string containing a expression to be matched with all chromosomes files (e.g."Chrom" for files which start by "Chrom" followed by the chromosome number).
`snpInfoDir`	[character]: character string naming a directory containing the reference data in a PLINK format (.bed, .bim and *.fam).
`signalFile`	[character]: the name of the signal file which the data are to be read from (2 columns: "SNP" and "PVALUE"). Each row of the table appears as one line of the file. If it does not contain an `_absolute_` path, the file name is `_relative_` to the current working directory, `getwd`. The fields separator character have to be a space `" "` or a tabulation `"\t"`.
`mc.cores`	[numeric]: the number of cores to use (default is `mc.cores=1`), i.e. at most how many child processes will be run simultaneously. Must be at least one, and parallelization requires at least two cores.

This function writes several files, in the temporary directory (defined in R_SESSION_TMPDIR), nothing else is returned. These files are used to build an Enrichment object by readEnrichment in order to compute enrichment analysis (reSample).

Mickael Canouil mickael.canouil@good.ibl.fr

Overview : snpEnrichment-package
Classes : Enrichment, Chromosome, EnrichSNP
Methods : plot, reSample, getEnrichSNP, excludeSNP, compareEnrichment,
enrichment, is.enrichment, chromosome, is.chromosome
Functions : initFiles, writeLD, readEnrichment

## Not run: snpInfoDir <- system.file("extdata/snpInfo",
                          package = "snpEnrichment")
signalFile <- system.file("extdata/Signal/toySignal.txt",
                          package = "snpEnrichment")
initFiles(pattern = "Chrom",
          snpInfoDir,
          signalFile,
          mc.cores = 1)
## End(Not run)