snpEnrichment (version 1.2-3)

readEnrichment: Read and create EnrichmentRatio object

Description

Read files created by initFiles and create an Enrichment object.

Usage

readEnrichment(pattern = "Chrom", signalFile, 
               transcriptFile = "FALSE", snpListDir, 
               snpInfoDir, distThresh = 1000, 
               sigThresh = 0.05, LD = FALSE, ldDir = NULL,
               extendMethod = "ld", mc.cores = 1)

Arguments

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 _re

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 each 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. 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 functions. Note that, this setting can increase the computation's time, depending on number of SNPs in the si

ldDir

[character]: character string naming a directory where the linkage Disequilibrium files should be written (default ldDir=NULL is in temporary directory).

extendMethod

[character]: character string naming the method to be used to extend the list of eSNPs. Default is "ld", the list of eSNPs is extended with all SNPs in LD (r^2 threshold, defined in writeLD). Other

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.

Value

• Return an object of class Enrichment partly filled.

See Also

Overview : snpEnrichment-package Classes : Enrichment, Chromosome, EnrichSNP Methods : plot, reSample, excludeSNP, compareEnrichment, enrichment, is.enrichment, chromosome, is.chromosome Functions : initFiles, writeLD, readEnrichment

Examples

snpListDir <- system.file("extdata/List", 
                          package = "snpEnrichment")
signalFile <- system.file("extdata/Signal/toySignal.txt", 
                          package = "snpEnrichment")
excludeFile <- system.file("extdata/Exclude/toyExclude.txt", 
                           package = "snpEnrichment")
snpInfoDir <- system.file("extdata/snpInfo", package = "snpEnrichment")
data(transcript)
transcriptFile <- transcript

toy_M1 <- readEnrichment(pattern = "Chrom", 
                         signalFile, 
                         transcriptFile, 
                         snpListDir, 
                         snpInfoDir, 
                         distThresh = 1000, 
                         sigThresh = 0.05, 
                         LD = FALSE, 
                         ldDir = NULL, 
                         extendMethod = "ld", 
                         mc.cores = 1)
toy_M1