Description Usage Arguments Value Note Author(s) See Also Examples
writeLD
write a '.ld' file for each chromosomes which contains the LD (r^2).
1 2 3 |
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 |
ldDir |
[character]: character string naming a directory where the linkage Disequilibrium files should be written (default |
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 |
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.
Mickael Canouil mickael.canouil@good.ibl.fr
Overview : snpEnrichment-package
Classes : Enrichment
, Chromosome
, EnrichSNP
Methods : plot
, reSample
, getEnrichSNP
, excludeSNP
, compareEnrichment
,
enrichment
, is.enrichment
, chromosome
, is.chromosome
Functions : initFiles
, writeLD
, readEnrichment
1 2 3 4 5 6 7 | ## 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)
|
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