compareEnrichment: Compare enrichment analysis between two SNPs list

In snpEnrichment: SNPs Enrichment Analysis

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 = TRUE,
                  mc.cores = 1, onlyGenome = TRUE)

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=TRUE (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=TRUE (default) compute resampling step for all chromosomes.

Value

Return a list of three elements:

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

Note

Still in development.

Author(s)

Mickael Canouil [e-mail]

See Also

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

Examples

## Not run: data(toyEnrichment)

reSample(object = toyEnrichment,
         nSample = 10,
         empiricPvalue = TRUE,
         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"
)
# OR
excludeFile <- system.file("extdata/Exclude/toyExclude.txt",
                           package = "snpEnrichment")

toyEnrichment_exclude <- excludeSNP(toyEnrichment, excludeFile, mc.cores = 1)

compareResults <- compareEnrichment(object.x = toyEnrichment,
                                    object.y = toyEnrichment_exclude,
                                    pattern = "Chrom",
                                    nSample = 10,
                                    empiricPvalue = FALSE,
                                    mc.cores = 1,
                                    onlyGenome = TRUE)
## End(Not run)

snpEnrichment documentation built on May 2, 2019, 8:44 a.m.