snpEnrichment (version 1.1-3)

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, 
        ldThresh = 0.8, onlySignal = TRUE,
        mc.cores = detectCores())

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 _re

ldThresh

[numeric]: threshold value for LD calculation (PLINK).

onlySignal

[logical]: onlySignal=TRUE (default) to compute LD for SNPs in signal (signalFile). Otherwise onlySignal=FALSE to compute linkage disequilibrium for all SNPs in reference data (snpInfoDir).

mc.cores

[numeric]: The number of cores to use, i.e. at most how many child processes will be run simultaneously. The option is initialized with detectCores. Must be at least one, and parallelization requires at least two cores.

Value

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

See Also

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

Examples

## Not run:
# signalFile <- "./extData/Signal/toySignal.txt"
# snpInfoDir <- "./extData/snpInfo/"
# snpListDir <- "./extData/List/"
# writeLD(pattern = "Chrom", snpInfoDir, signalFile, 
#         ldThresh = 0.8, onlySignal = TRUE, 
#         mc.cores = detectCores())
## End (Not run)