Read files created by initFiles and create an Enrichment object.
readEnrichment(pattern = "Chrom", signalFile, transcriptFile = FALSE, snpListDir, snpInfoDir, distThresh = 1000, sigThresh = 0.05, LD = FALSE, ldDir = NULL, mc.cores = 1)
pattern | A character string containing a expression to be matched with all chromosomes files
(e.g., |
---|---|
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 |
transcriptFile | A character string naming a file or a data.frame with four columns:
Chromomosome, trancript's name, Starting and Ending positions.
|
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.
if (interactive()) { 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 }