compareEnrichment: Compare enrichment analysis between two SNPs list
In mcanouil/snpEnrichment: SNPs Enrichment Analysis With Sampling

Description Usage Arguments Value Note Examples

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

1 2	compareEnrichment(object.x, object.y, pattern = "Chrom", nSample = 100, empiricPvalue = TRUE, mc.cores = 1, onlyGenome = TRUE)

`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`).

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.

Still in development.

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
  )
}