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.
initFiles(pattern = "Chrom", snpInfoDir, signalFile, mc.cores = 1)
pattern | A character string containing a expression to be matched with all chromosomes files
(e.g., |
---|---|
snpInfoDir | character: character string naming a directory containing the reference data in a PLINK format (.bed, .bim and .fam). |
signalFile | 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 |
mc.cores | numeric: the number of cores to use (default is |
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).
if (interactive()) { snpInfoDir <- system.file("extdata/snpInfo", package = "snpEnrichment") signalFile <- system.file("extdata/Signal/toySignal.txt", package = "snpEnrichment") initFiles(pattern = "Chrom", snpInfoDir, signalFile, mc.cores = 1) }