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).

Author
Mickael Canouil [aut, cre], Loic Yengo [ctb]
Date of publication
2015-10-01 23:18:57
Maintainer
Mickael Canouil <mickael.canouil@cnrs.fr>
License
GPL (>= 2)
Version
1.7.0
URLs

View on CRAN

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

Files in this package

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