excludeSNP-methods: Exclude SNPs from Enrichment analysis

In snpEnrichment: SNPs Enrichment Analysis

Description

Remove a specify set of SNPs and compute a new enrichment analysis.

Usage

excludeSNP(object, excludeFile, mc.cores = 1)

Arguments

object	[Enrichment]: an Enrichment object filled by reSample.
excludeFile	[vector(character)]: a list of SNPs to remove from a previous enrichment analysis. A path to a file which the first column are the SNPs.
mc.cores	[numeric]: the number of cores to use (default is mc.cores=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.

Value

Return the object given in argument where lists of SNPs are updated by removing SNPs in excludeFile.

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

## Not run: data(toyEnrichment)
excludeFile <- c(
    "rs4376885", "rs17690928", "rs6460708", "rs13061537", "rs11769827",
    "rs12717054", "rs2907627", "rs1380109", "rs7024214", "rs7711972",
    "rs9658282", "rs11750720", "rs1793268", "rs774568", "rs6921786",
    "rs1699031", "rs6994771", "rs16926670", "rs465612", "rs3012084",
    "rs354850", "rs12803455", "rs13384873", "rs4364668", "rs8181047",
    "rs2179993", "rs12049335", "rs6079926", "rs2175144", "rs11564427",
    "rs7786389", "rs7005565", "rs17423335", "rs12474102", "rs191314",
    "rs10513168", "rs1711437", "rs1992620", "rs283115", "rs10754563",
    "rs10851727", "rs2173191", "rs7661353", "rs1342113", "rs7042073",
    "rs1567445", "rs10120375", "rs550060", "rs3761218", "rs4512977"
)
# OR
excludeFile <- system.file("extdata/Exclude/toyExclude.txt",
                           package = "snpEnrichment")

toyEnrichment_exclude <- excludeSNP(toyEnrichment, excludeFile, mc.cores = 1)
toyEnrichment_exclude
## End(Not run)

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