snpEnrichment (version 1.1-3)

excludeSNP: Exclude SNPs from Enrichment analysis

Description

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

Usage

excludeSNP(object, excludeFile, nSample = 100, sigThresh = 0.05, 
           MAFpool = c(0.05, 0.10, 0.2, 0.3, 0.4, 0.5), 
           extendMethod = "ld", mc.cores = detectCores())

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.

nSample

[numeric]: the number of resampling done by reSample for p-values computation (minimum is 100).

sigThresh

[numeric]: statistical threshold for signal (e.g. sigThresh = 0.05 for a given GWAS signal) used to compute an Enrichment Ratio.

MAFpool

[vector(numeric)]: either a numeric vector giving the breaks points of intervals into which SNP's MAF (Minor Allele Frequency) is to be split.

extendMethod

[character]: character string naming the method to be used to extend the list of eSNPs. Default is "ld", the list of eSNPs is extended with all SNPs in LD (r^2 threshold, defined in initFiles). O

mc.cores

[numeric]: The number of cores to use, i.e. at most how many child processes will be run simultaneously. The option is initialized with detectCores. 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.

See Also

Overview : snpEnrichment-package Classes : Enrichment, Chromosome, SNP Methods : plot, reSample, excludeSNP, compareEnrichment, enrichment, is.enrichment, chromosome, is.chromosome Functions : initFiles, writeLD, readEnrichment

Examples

# data(toyM1) # data(toyM2)
# excludeFile <- c(
    # "rs1561385", "rs7792796", "rs2514670", "rs9641913", "rs8184976",
    # "rs17582442", "rs7690663", "rs4940941", "rs7069561", "rs540218",
    # "rs17315714", "rs17795475", "rs7171423", "rs2392927", "rs12593911",
    # "rs4150477", "rs11608342", "rs16998578", "rs4299828", "rs915865",
    # "rs10976361", "rs7863276", "rs16908503", "rs544845", "rs1473462",
    # "rs4757541", "rs7640480", "rs7121036", "rs6803546", "rs10851981",
    # "rs4724502", "rs9540053", "rs10935849", "rs11193005", "rs6566417",
    # "rs1693294", "rs12759271", "rs17718970", "rs4774717", "rs455839",
    # "rs942278", "rs6545708", "rs7557832", "rs1498356", "rs11083318",
    # "rs9595937", "rs1561476", "rs12188654", "rs2048839", "rs4689801"
# )

# toyM1_exclude <- excludeSNP(toyM1, 
                            # excludeFile, 
                            # nSample = 10, 
                            # sigThresh = 0.05, 
                            # MAFpool = c(0.05, 0.10, 0.2, 0.3, 0.4, 0.5),
                            # extendMethod = "ld",
                            # mc.cores = detectCores())
# toyM1_exclude