snpEnrichment (version 1.2-3)

compareEnrichment: Compare enrichment analysis between two SNPs list

Description

Compare the enrichment analysis between two set of SNPs. compareEnrichment compare two files with list of SNPs or two Enrichment objects.

Usage

compareEnrichment(object.x, object.y, pattern = "Chrom",
                  nSample = 100, mc.cores = 1, onlyGenome = FALSE)

Arguments

object.x, object.y

[character or Enrichment]: character string naming a directory containing a list of SNPs for each chromosomes or an Enrichment object (fully filled, e.g. results from rea

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).

nSample

[numeric]: the number of resampling done by reSample for p-values computation (minimum is 100).

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.

onlyGenome

[logical]: onlyGenome=FALSE (default) compute resampling step for all chromosomes.

Value

• Return a list of three elements:
• summary
  Two data.frame which summarize for eSNP and/or xSNP the enrichment analyses and the comparison between them.
• object1
  Enrichment object of from List1.
• object2
  Enrichment object of from List2.

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

data(toyEnrichmentM1)

reSample(object = toyEnrichmentM1, 
         nSample = 10, 
         MAFpool = c(0.05, 0.10, 0.2, 0.3, 0.4, 0.5), 
         mc.cores = 1,
         onlyGenome = TRUE)

excludeFile <- c(
    "rs7897180", "rs4725479", "rs315404", "rs17390391", "rs1650670",
    "rs6783390", "rs1642009", "rs4756586", "rs11995037", "rs4977345",
    "rs13136448", "rs4233536", "rs11151079", "rs2299657", "rs4833930",
    "rs1384", "rs7168184", "rs6909895", "rs7972667", "rs2293229",
    "rs918216", "rs6040608", "rs2817715", "rs13233541", "rs4486743",
    "rs2127806", "rs10912854", "rs1869052", "rs9853549", "rs448658",
    "rs2451583", "rs17483288", "rs10962314", "rs9612059", "rs1384182",
    "rs8049208", "rs12215176", "rs2980996", "rs1736976", "rs8089268",
    "rs10832329", "rs12446540", "rs7676237", "rs869922", "rs16823426",
    "rs1374393", "rs13268781", "rs11134505", "rs7325241", "rs7520109"
)

toyM1_exclude <- excludeSNP(toyEnrichmentM1, excludeFile, mc.cores = 1)

compareResults <- compareEnrichment(object.x = toyEnrichmentM1, 
                                    object.y = toyM1_exclude, 
                                    pattern = "Chrom", 
                                    nSample = 10, 
                                    mc.cores = 1, 
                                    onlyGenome = TRUE)