Compare enrichment analysis between two SNPs list

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

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

Arguments

object.x	An Enrichment object fully filled (e.g., readEnrichment).
object.y	An Enrichment object fully filled (e.g., readEnrichment).
pattern	A 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	The number of resampling done by reSample for p-values computation (minimum is 100).
empiricPvalue	Compute PValue based on the null distribution (FALSE). If TRUE (default), the empirical p-values are computed instead.
mc.cores	numeric: the number of cores to use (default is 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	Compute resampling step for all chromosomes (default TRUE).

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.

Examples

if (interactive()) {
  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
  )
}