R/compareEnrichment.R
compareEnrichment.Rd
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)
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., |
nSample | The number of resampling done by reSample for p-values computation (minimum is |
empiricPvalue | Compute PValue based on the null distribution ( |
mc.cores | numeric: the number of cores to use (default is |
onlyGenome | Compute resampling step for all chromosomes (default |
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 ) }