snpEnrichment: SNPs Enrichment Analysis
Version 1.7.0

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

Browse man pages Browse package API and functions Browse package files

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
URL https://github.com/mcanouil/snpEnrichment
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("snpEnrichment")

Man pages

Chromosome-class: Class 'Chromosome'
compareEnrichment: Compare enrichment analysis between two SNPs list
Enrichment-class: Class 'Enrichment'
EnrichSNP-class: Class '"EnrichSNP"'
excludeSNP-methods: Exclude SNPs from Enrichment analysis
GC: Full Garbage Collection
getEnrichSNP-methods: Get all eSNP/xSNP which are enriched
initFiles: Initialize files for enrichment analysis
is.chromosome: Is an Chromosome object
is.enrichment: Is an Enrichment object
mclapply2: Parallel Versions of 'lapply' with cores and memory control
plot-methods: Plot method (S4) for 'Enrichment' object
print-methods: Print method (S4)
readEnrichment: Read and create EnrichmentRatio object
reSample-methods: Compute enrichment analysis on an 'Enrichment' object
snpEnrichment-internal: ~ Internal: snpEnrichment objects and methods ~
snpEnrichment-package: ~ Overview: SNPs enrichment analysis ~
toyEnrichment-dataset: Toy dataset with SNP data
transcript-dataset: Transcript information in order to check the CIS status for...
writeLD: Linkage Disequilibrium (LD) computation with PLINK

Functions

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

Files

inst
inst/example.R
inst/extdata
inst/extdata/Signal
inst/extdata/Signal/toySignal.txt
inst/extdata/List
inst/extdata/List/Chrom15-toyList.txt
inst/extdata/List/Chrom18-toyList.txt
inst/extdata/List/Chrom6-toyList.txt
inst/extdata/List/Chrom21-toyList.txt
inst/extdata/List/Chrom3-toyList.txt
inst/extdata/List/Chrom2-toyList.txt
inst/extdata/List/Chrom4-toyList.txt
inst/extdata/List/Chrom7-toyList.txt
inst/extdata/List/Chrom8-toyList.txt
inst/extdata/List/Chrom12-toyList.txt
inst/extdata/List/Chrom20-toyList.txt
inst/extdata/List/Chrom10-toyList.txt
inst/extdata/List/Chrom9-toyList.txt
inst/extdata/List/Chrom19-toyList.txt
inst/extdata/List/Chrom14-toyList.txt
inst/extdata/List/Chrom22-toyList.txt
inst/extdata/List/Chrom13-toyList.txt
inst/extdata/List/Chrom11-toyList.txt
inst/extdata/List/Chrom17-toyList.txt
inst/extdata/List/Chrom5-toyList.txt
inst/extdata/List/Chrom1-toyList.txt
inst/extdata/List/Chrom16-toyList.txt
inst/extdata/Exclude
inst/extdata/Exclude/toyExclude.txt
inst/extdata/snpInfo
inst/extdata/snpInfo/Chrom6-toy.fam
inst/extdata/snpInfo/Chrom9-toy.bim
inst/extdata/snpInfo/Chrom11-toy.fam
inst/extdata/snpInfo/Chrom17-toy.bim
inst/extdata/snpInfo/Chrom5-toy.bim
inst/extdata/snpInfo/Chrom15-toy.fam
inst/extdata/snpInfo/Chrom21-toy.bed
inst/extdata/snpInfo/Chrom21-toy.fam
inst/extdata/snpInfo/Chrom3-toy.bim
inst/extdata/snpInfo/Chrom18-toy.bim
inst/extdata/snpInfo/Chrom20-toy.bed
inst/extdata/snpInfo/Chrom4-toy.fam
inst/extdata/snpInfo/Chrom5-toy.bed
inst/extdata/snpInfo/Chrom12-toy.bim
inst/extdata/snpInfo/Chrom4-toy.bim
inst/extdata/snpInfo/Chrom22-toy.fam
inst/extdata/snpInfo/Chrom15-toy.bim
inst/extdata/snpInfo/Chrom20-toy.fam
inst/extdata/snpInfo/Chrom9-toy.bed
inst/extdata/snpInfo/Chrom1-toy.bed
inst/extdata/snpInfo/Chrom15-toy.bed
inst/extdata/snpInfo/Chrom2-toy.fam
inst/extdata/snpInfo/Chrom13-toy.bim
inst/extdata/snpInfo/Chrom14-toy.bed
inst/extdata/snpInfo/Chrom21-toy.bim
inst/extdata/snpInfo/Chrom8-toy.bim
inst/extdata/snpInfo/Chrom10-toy.fam
inst/extdata/snpInfo/Chrom16-toy.bed
inst/extdata/snpInfo/Chrom14-toy.bim
inst/extdata/snpInfo/Chrom2-toy.bim
inst/extdata/snpInfo/Chrom14-toy.fam
inst/extdata/snpInfo/Chrom19-toy.fam
inst/extdata/snpInfo/Chrom7-toy.bim
inst/extdata/snpInfo/Chrom17-toy.bed
inst/extdata/snpInfo/Chrom9-toy.fam
inst/extdata/snpInfo/Chrom1-toy.bim
inst/extdata/snpInfo/Chrom12-toy.fam
inst/extdata/snpInfo/Chrom11-toy.bim
inst/extdata/snpInfo/Chrom16-toy.bim
inst/extdata/snpInfo/Chrom8-toy.fam
inst/extdata/snpInfo/Chrom4-toy.bed
inst/extdata/snpInfo/Chrom2-toy.bed
inst/extdata/snpInfo/Chrom1-toy.fam
inst/extdata/snpInfo/Chrom3-toy.fam
inst/extdata/snpInfo/Chrom10-toy.bim
inst/extdata/snpInfo/Chrom18-toy.bed
inst/extdata/snpInfo/Chrom6-toy.bed
inst/extdata/snpInfo/Chrom19-toy.bed
inst/extdata/snpInfo/Chrom16-toy.fam
inst/extdata/snpInfo/Chrom6-toy.bim
inst/extdata/snpInfo/Chrom8-toy.bed
inst/extdata/snpInfo/Chrom18-toy.fam
inst/extdata/snpInfo/Chrom5-toy.fam
inst/extdata/snpInfo/Chrom10-toy.bed
inst/extdata/snpInfo/Chrom17-toy.fam
inst/extdata/snpInfo/Chrom13-toy.fam
inst/extdata/snpInfo/Chrom12-toy.bed
inst/extdata/snpInfo/Chrom22-toy.bed
inst/extdata/snpInfo/Chrom3-toy.bed
inst/extdata/snpInfo/Chrom19-toy.bim
inst/extdata/snpInfo/Chrom7-toy.fam
inst/extdata/snpInfo/Chrom7-toy.bed
inst/extdata/snpInfo/Chrom13-toy.bed
inst/extdata/snpInfo/Chrom22-toy.bim
inst/extdata/snpInfo/Chrom11-toy.bed
inst/extdata/snpInfo/Chrom20-toy.bim
tests
tests/RUN-TEST_snpEnrichment.R
NAMESPACE
data
data/toyEnrichment.RData
data/transcript.txt.xz
R
R/chromosome.R
R/enrichment.R
R/Global.R
R/SNP.R
MD5
DESCRIPTION
ChangeLog
man
man/getEnrichSNP-methods.Rd
man/snpEnrichment-internal.Rd
man/Enrichment-class.Rd
man/plot-methods.Rd
man/mclapply2.Rd
man/snpEnrichment-package.Rd
man/is.enrichment.Rd
man/compareEnrichment.Rd
man/initFiles.Rd
man/toyEnrichment-dataset.Rd
man/readEnrichment.Rd
man/reSample-methods.Rd
man/writeLD.Rd
man/GC.Rd
man/transcript-dataset.Rd
man/Chromosome-class.Rd
man/print-methods.Rd
man/is.chromosome.Rd
man/excludeSNP-methods.Rd
man/EnrichSNP-class.Rd
snpEnrichment documentation built on May 19, 2017, 9:24 p.m.