readEnrichment: Read and create EnrichmentRatio object
In snpEnrichment: SNPs Enrichment Analysis

Description Usage Arguments Value Author(s) See Also Examples

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`	[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 `_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"`.
`transcriptFile`	[character or data.frame]: character string naming a file or a `data.frame` with four columns: Chromomosome, trancript's name, Starting and Ending positions. `data(trancript)` can be use as parameters. Default is `FALSE`.
`snpListDir`	[character]: character string naming a directory containing a list of SNPs for one or several chromosomes. `snpListDir` can be a single file with at least two columns: chromosome and rs name.
`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. `distThresh` is used if `transcriptFile` is set.
`sigThresh`	[numeric]: statistical threshold for signal (e.g. `sigThresh = 0.05` for a given GWAS signal) used to compute an Enrichment Ratio.
`LD`	[logical]: `LD=TRUE` (default is `FALSE`) read LD compute with `writeLD` function or with PLINK. Note that, this setting can increase the computation's time, depending on number of SNPs in the signal file.
`ldDir`	[character]: character string naming a directory where the linkage disequilibrium files should be read (default `ldDir=NULL` is in temporary directory). LD files can be the LD output from plink.
`mc.cores`	[numeric]: the number of cores to use (default is `mc.cores=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.

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

## 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)