snpEnrichment: SNPs Enrichment Analysis

Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).

AuthorMickael Canouil [aut, cre], Loic Yengo [ctb]
Date of publication2015-10-01 23:18:57
MaintainerMickael Canouil <mickael.canouil@cnrs.fr>
LicenseGPL (>= 2)
Version1.7.0
https://github.com/mcanouil/snpEnrichment

View on CRAN

Functions

.checkFilePath Man page
.checkSignalFile Man page
.checkSnpInfoDir Man page
.checkSnpListDir Man page
.checkTranscript Man page
chromosome Man page
Chromosome Man page
chromosome,ANY,ANY,ANY,ANY-method Man page
[<-,Chromosome,ANY,ANY,ANY-method Man page
[,Chromosome,ANY,ANY,ANY-method Man page
chromosome,ANY-method Man page
Chromosome-class Man page
[<-,Chromosome-method Man page
[,Chromosome-method Man page
chromosome-methods Man page
.Chromosome.show Man page
.cleanTmpDir Man page
.compareEnrich Man page
compareEnrichment Man page
compareEnrichment,ANY,ANY,ANY,ANY,ANY,ANY-method Man page
compareEnrichment,ANY-method Man page
compareEnrichment,Enrichment,Enrichment,ANY-method Man page
compareEnrichment-methods Man page
computeER Man page
computeER,ANY-method Man page
computeER,Chromosome-method Man page
computeER,Chromosome-method Man page
computeER,Enrichment-method Man page
computeER,Enrichment-method Man page
doLDblock Man page
doLDblock,ANY-method Man page
doLDblock,Chromosome-method Man page
doLDblock,Chromosome-method Man page
enrichment Man page
Enrichment Man page
enrichment,ANY,ANY,ANY,ANY,ANY-method Man page
[<-,Enrichment,ANY,ANY,ANY-method Man page
[,Enrichment,ANY,ANY,ANY-method Man page
enrichment,ANY-method Man page
Enrichment-class Man page
[<-,Enrichment-method Man page
[,Enrichment-method Man page
enrichment-methods Man page
.enrichmentRatio Man page
.Enrichment.show Man page
enrichSNP Man page
EnrichSNP Man page
EnrichSNP Man page
EnrichSNP,ANY,ANY,ANY,ANY,ANY,ANY-method Man page
[<-,EnrichSNP,ANY,ANY,ANY-method Man page
[,EnrichSNP,ANY,ANY,ANY-method Man page
enrichSNP,ANY-method Man page
EnrichSNP-class Man page
[<-,EnrichSNP-method Man page
[,EnrichSNP-method Man page
enrichSNP-methods Man page
EnrichSNP-methods Man page
.EnrichSNP.show Man page
excludeSNP Man page
excludeSNP,ANY,ANY,ANY,ANY,ANY,ANY,ANY-method Man page
excludeSNP,ANY-method Man page
excludeSNP,Enrichment,ANY-method Man page
excludeSNP,Enrichment-method Man page
excludeSNP,Enrichment-method Man page
excludeSNP-methods Man page
GC Man page
getEnrichSNP Man page
getEnrichSNP,ANY-method Man page
getEnrichSNP,Enrichment,ANY-method Man page
getEnrichSNP,Enrichment-method Man page
getEnrichSNP-methods Man page
initFiles Man page
is.chromosome Man page
is.chromosome,ANY-method Man page
is.chromosome-methods Man page
is.enrichment Man page
is.enrichment,ANY-method Man page
is.enrichment-methods Man page
is.EnrichSNP Man page
is.EnrichSNP,ANY-method Man page
is.EnrichSNP-methods Man page
mclapply2 Man page
plot Man page
plot,Enrichment,ANY-method Man page
plot,Enrichment-method Man page
plot-methods Man page
print Man page
print,Chromosome,ANY,ANY-method Man page
print,Chromosome-method Man page
print,Chromosome-method Man page
print,Enrichment,ANY,ANY-method Man page
print,Enrichment-method Man page
print,Enrichment-method Man page
print,EnrichSNP-method Man page
print-methods Man page
readEnrichment Man page
.readFiles Man page
.readFreq Man page
.readLD Man page
.readSignal Man page
.readSNP Man page
.readTranscript Man page
reSample Man page
.reSample Man page
reSample,ANY-method Man page
reSample,Chromosome,ANY,ANY,ANY,ANY,ANY-method Man page
reSample,Chromosome,ANY-method Man page
reSample,Chromosome-method Man page
reSample,Chromosome-method Man page
reSample,Enrichment,ANY,ANY,ANY,ANY,ANY-method Man page
reSample,Enrichment,ANY-method Man page
reSample,Enrichment-method Man page
reSample,Enrichment-method Man page
reSample-methods Man page
reset Man page
reset,ANY-method Man page
reset,Chromosome,ANY-method Man page
reset,Chromosome-method Man page
reset,Chromosome-method Man page
reset,Enrichment,ANY-method Man page
reset,Enrichment-method Man page
reset,Enrichment-method Man page
reset,EnrichSNP,ANY-method Man page
reset,EnrichSNP-method Man page
reset-methods Man page
.showArgs Man page
.showArgs Man page
.showArgs Man page
show,Chromosome-method Man page
show,Enrichment-method Man page
show,EnrichSNP-method Man page
snpEnrichment Man page
snpEnrichment-package Man page
.splitByChrom Man page
toyEnrichment Man page
toyEnrichment-dataset Man page
transcript Man page
transcript-dataset Man page
.verbose Man page
.verbose Man page
.writeFreq Man page
.writeFreq Man page
writeLD Man page
.writeSignal Man page
.writeSignal Man page

Files

snpEnrichment
snpEnrichment/inst
snpEnrichment/inst/example.R
snpEnrichment/inst/extdata
snpEnrichment/inst/extdata/Signal
snpEnrichment/inst/extdata/Signal/toySignal.txt
snpEnrichment/inst/extdata/List
snpEnrichment/inst/extdata/List/Chrom15-toyList.txt
snpEnrichment/inst/extdata/List/Chrom18-toyList.txt
snpEnrichment/inst/extdata/List/Chrom6-toyList.txt
snpEnrichment/inst/extdata/List/Chrom21-toyList.txt
snpEnrichment/inst/extdata/List/Chrom3-toyList.txt
snpEnrichment/inst/extdata/List/Chrom2-toyList.txt
snpEnrichment/inst/extdata/List/Chrom4-toyList.txt
snpEnrichment/inst/extdata/List/Chrom7-toyList.txt
snpEnrichment/inst/extdata/List/Chrom8-toyList.txt
snpEnrichment/inst/extdata/List/Chrom12-toyList.txt
snpEnrichment/inst/extdata/List/Chrom20-toyList.txt
snpEnrichment/inst/extdata/List/Chrom10-toyList.txt
snpEnrichment/inst/extdata/List/Chrom9-toyList.txt
snpEnrichment/inst/extdata/List/Chrom19-toyList.txt
snpEnrichment/inst/extdata/List/Chrom14-toyList.txt
snpEnrichment/inst/extdata/List/Chrom22-toyList.txt
snpEnrichment/inst/extdata/List/Chrom13-toyList.txt
snpEnrichment/inst/extdata/List/Chrom11-toyList.txt
snpEnrichment/inst/extdata/List/Chrom17-toyList.txt
snpEnrichment/inst/extdata/List/Chrom5-toyList.txt
snpEnrichment/inst/extdata/List/Chrom1-toyList.txt
snpEnrichment/inst/extdata/List/Chrom16-toyList.txt
snpEnrichment/inst/extdata/Exclude
snpEnrichment/inst/extdata/Exclude/toyExclude.txt
snpEnrichment/inst/extdata/snpInfo
snpEnrichment/inst/extdata/snpInfo/Chrom6-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom9-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom11-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom17-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom5-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom15-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom21-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom21-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom3-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom18-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom20-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom4-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom5-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom12-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom4-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom22-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom15-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom20-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom9-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom1-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom15-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom2-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom13-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom14-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom21-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom8-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom10-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom16-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom14-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom2-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom14-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom19-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom7-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom17-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom9-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom1-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom12-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom11-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom16-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom8-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom4-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom2-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom1-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom3-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom10-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom18-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom6-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom19-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom16-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom6-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom8-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom18-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom5-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom10-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom17-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom13-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom12-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom22-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom3-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom19-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom7-toy.fam
snpEnrichment/inst/extdata/snpInfo/Chrom7-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom13-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom22-toy.bim
snpEnrichment/inst/extdata/snpInfo/Chrom11-toy.bed
snpEnrichment/inst/extdata/snpInfo/Chrom20-toy.bim
snpEnrichment/tests
snpEnrichment/tests/RUN-TEST_snpEnrichment.R
snpEnrichment/NAMESPACE
snpEnrichment/data
snpEnrichment/data/toyEnrichment.RData
snpEnrichment/data/transcript.txt.xz
snpEnrichment/R
snpEnrichment/R/chromosome.R snpEnrichment/R/enrichment.R snpEnrichment/R/Global.R snpEnrichment/R/SNP.R
snpEnrichment/MD5
snpEnrichment/DESCRIPTION
snpEnrichment/ChangeLog
snpEnrichment/man
snpEnrichment/man/getEnrichSNP-methods.Rd snpEnrichment/man/snpEnrichment-internal.Rd snpEnrichment/man/Enrichment-class.Rd snpEnrichment/man/plot-methods.Rd snpEnrichment/man/mclapply2.Rd snpEnrichment/man/snpEnrichment-package.Rd snpEnrichment/man/is.enrichment.Rd snpEnrichment/man/compareEnrichment.Rd snpEnrichment/man/initFiles.Rd snpEnrichment/man/toyEnrichment-dataset.Rd snpEnrichment/man/readEnrichment.Rd snpEnrichment/man/reSample-methods.Rd snpEnrichment/man/writeLD.Rd snpEnrichment/man/GC.Rd snpEnrichment/man/transcript-dataset.Rd snpEnrichment/man/Chromosome-class.Rd snpEnrichment/man/print-methods.Rd snpEnrichment/man/is.chromosome.Rd snpEnrichment/man/excludeSNP-methods.Rd snpEnrichment/man/EnrichSNP-class.Rd

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