writeLD write a '.ld' file for each chromosomes which contains the LD (r^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., |
---|---|
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 |
ldDir | character: character string naming a directory where the linkage disequilibrium files
should be read (default |
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 |
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) }