snpEnrichment (version 1.7.0)

Enrichment-class: Class Enrichment

Description

This class is defined to summarize the enrichment analysis on each chromosomes and the whole genome.

Objects from the Class

enrichment is defined to build an object of class Enrichment in order to compute an enrichment analysis. Enrichment is the object containing the results for all Chromosome object and for the whole genome. When an Enrichment object is created, it contains a list of SNPs (e.g. eSNPs). All the others slots are "empty". After reSample is ran on an Enrichment object, the slots: Table, EnrichmentRatio, Z, PValue and Resampling are filled.

Note that if reSample is executed on an Enrichment every new resampling is added to the original ones, pre-existing statistics are erased and computed again with the new resampling set.

Extends

Class Chromosome, directly. Class EnrichSNP, directly.

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

data(toyEnrichment)
toyEnrich <- enrichment()
show(toyEnrich)

toyEnrich["Loss"] <- toyEnrichment["Loss"]
toyEnrich["Loss"]

toyEnrich <- enrichment(Loss = toyEnrichment["Loss"],
                        eSNP = toyEnrichment["eSNP"])
toyEnrich <- enrichment(Loss = toyEnrichment["Loss"])

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)
print(toyEnrichment)

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"
)

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