writeLD: Linkage Disequilibrium (LD) computation with PLINK
In mcanouil/snpEnrichment: SNPs Enrichment Analysis With Sampling

Description Usage Arguments Value Note Examples

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

1 2	writeLD(pattern = "Chrom", snpInfoDir, signalFile, ldDir = NULL, ldThresh = 0.8, depth = 1000, mc.cores = 1)

`pattern`	A 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`	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 read (default `NULL` is in temporary directory). LD files can be the LD output from plink.
`ldThresh`	Threshold value for LD calculation.
`depth`	This parameter is mandatory and controls the maximum lag between SNPs considered.
`mc.cores`	numeric: the number of cores to use (default is `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.

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

The LD computation can take a long time depending on number of SNPs in signalFile. It is recommended to save LD results in a directory (ldDir) which is not a temporary directory.

if (interactive()) {
  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)
}