snpEnrichment (version 1.4-1)

compareEnrichment: Compare enrichment analysis between two SNPs list

Description

Compare the enrichment analysis between two set of SNPs. compareEnrichment compare two Enrichment objects.

Usage

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

Arguments

object.x, object.y

[Enrichment]: an Enrichment object fully filled (e.g. readEnrichment).

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).

empiricPvalue

[logical]: empiricPvalue=FALSE (default) compute PValue based on the null distribution (resampling). If empiricPvalue=TRUE, the empirical p-values are computed instead.

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 passed in object.x with resampling data.
• object2
  Enrichment object passed in object.y with resampling data.
• comparison
  Enrichment object from the comparison between object.x and object.y.

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(toyEnrichment)

reSample(object = toyEnrichment,
         nSample = 10,
         empiricPvalue = FALSE,
         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(toyEnrichment, excludeFile, mc.cores = 1)

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