Enrichment-class: Class 'Enrichment'

In snpEnrichment: SNPs Enrichment Analysis

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.

Slots

Loss

[data.frame]: a four columns data.frame: "Rows", "Unique", "Intersect.Ref.Signal" and "CIS". This slot gives information on data losses.

Call

[list]: each parameters used for the reading or resampling step are stored in this slot.

eSNP, xSNP

[SNP]: contain a EnrichSNP object (whith slots: SNP, Table, EnrichmentRatio, Z, PValue and Resampling) for a list of SNPs (eSNP) and an extended one (xSNP).

Chromosomes

[list(Chromosome)]: a list of 22 Chromosome objects.

Extends

Class Chromosome, directly.
Class EnrichSNP, directly.

Methods

enrichment(Loss, Call, eSNP, xSNP, Chromosomes):

Generate and initialize a new Enrichment object.

object["slotName"]:

Get the value of the field slotName.

object["slotName"]<-value:

Set value to the field slotName.

show(object):

Return the formatted values of Enrichment object.

print(object, what, type):

Return a summary table of an Enrichment object.

reSample(object, nSample, MAFpool, mc.cores, onlyGenome):

Compute P-Values based upon a resampling of SNPs (eSNP and xSNP) and update the Enrichment object.

excludeSNP(object, excludeFile, mc.cores):

Excludes SNPs given in excludeFile from the original list of eSNPs (xSNPs). Then a new enrichment analysis is computed.

reset(object, "slotName"):

Reset the field slotName.

plot(object, what, type, ggplot, pvalue):

Plot p-values or Z-statistics convergence.

getEnrichSNP(object, type):

Return eSNP/xSNP which are enriched as a data.frame.

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

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"])

## Not run: 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)
## End(Not run)

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