snpEnrichment (version 1.7.0)

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 _relative_ to the current working directory, getwd. The fields separator character have to be a space " " or a tabulation "\t".

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

## Not run: 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)## End(Not run)