Description Usage Arguments Value Author(s) See Also Examples
Read files created by initFiles
and create an Enrichment
object.
1 2 3 4 5 | readEnrichment(pattern = "Chrom", signalFile,
transcriptFile = "FALSE", snpListDir,
snpInfoDir, distThresh = 1000,
sigThresh = 0.05, LD = FALSE, ldDir = NULL,
mc.cores = 1)
|
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). |
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 |
transcriptFile |
[character or data.frame]: character string naming a file or a |
snpListDir |
[character]: character string naming a directory containing a list of SNPs for one or several chromosomes. |
snpInfoDir |
[character]: character string naming a directory containing the reference data in a PLINK format (*.bed, *.bim and *.fam). |
distThresh |
[numeric]: maximal distance (kb) between SNP and gene. |
sigThresh |
[numeric]: statistical threshold for signal (e.g. |
LD |
[logical]: |
ldDir |
[character]: character string naming a directory where the linkage disequilibrium files should be read (default |
mc.cores |
[numeric]: the number of cores to use (default is |
Return an object of class Enrichment
partly filled.
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 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## Not run: snpListDir <- system.file("extdata/List",
package = "snpEnrichment")
signalFile <- system.file("extdata/Signal/toySignal.txt",
package = "snpEnrichment")
snpInfoDir <- system.file("extdata/snpInfo", package = "snpEnrichment")
data(transcript)
transcriptFile <- transcript
initFiles(pattern = "Chrom", snpInfoDir, signalFile, mc.cores = 1)
toyData <- readEnrichment(pattern = "Chrom",
signalFile,
transcriptFile,
snpListDir,
snpInfoDir,
distThresh = 1000,
sigThresh = 0.05,
LD = FALSE,
ldDir = NULL,
mc.cores = 1)
toyData
## End(Not run)
|
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