snpEnrichment (version 1.6.0)

writeLD: Linkage Disequilibrium (LD) computation with PLINK

Description

writeLD write a '.ld' file for each chromosomes which contains the LD (r^2).

Usage

writeLD(pattern = "Chrom", snpInfoDir, signalFile,
        ldDir = NULL, ldThresh = 0.8, depth = 1000,
        mc.cores = 1)

Arguments

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 _rel

ldDir

[character]: character string naming a directory where the linkage Disequilibrium files should be written (default ldDir=NULL is in temporary directory).

ldThresh

[numeric]: threshold value for LD calculation.

depth

[numeric]: this parameter is mandatory and controls the maximum lag between SNPs considered.

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.

Value

• One ".ld" file per chromosome is returned by writeLD in snpInfoDir directory.

See Also

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

Examples

signalFile <- system.file("extdata/Signal/toySignal.txt",
                          package = "snpEnrichment")
snpInfoDir <- system.file("extdata/snpInfo",
                          package = "snpEnrichment")
writeLD(pattern = "Chrom", snpInfoDir, signalFile,
        ldDir = NULL, ldThresh = 0.8, mc.cores = 1)