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snpEnrichment (version 1.6.0)

SNPs Enrichment Analysis

Description

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

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Install

install.packages('snpEnrichment')

Monthly Downloads

6

Version

1.6.0

License

GPL (>= 2)

Issues

0

Pull Requests

0

Stars

3

Forks

2

Maintainer

Mickael Canouil

Last Published

November 4th, 2014

Functions in snpEnrichment (1.6.0)

plot-methods

Plot method (S4) for Enrichment object
excludeSNP

Exclude SNPs from Enrichment analysis
print-methods

Print method (S4)
readEnrichment

Read and create EnrichmentRatio object
snpEnrichment-internal

~ Internal: snpEnrichment objects and methods ~
reSample

Compute enrichment analysis on an Enrichment object
is.chromosome

Is an Chromosome object
writeLD

Linkage Disequilibrium (LD) computation with PLINK
Chromosome-class

Class Chromosome
GC

Full Garbage Collection
mclapply2

Parallel Versions of lapply with cores and memory control
is.enrichment

Is an Enrichment object
EnrichSNP-class

Class "EnrichSNP"
Enrichment-class

Class Enrichment
getEnrichSNP

Get all eSNP/xSNP which are enriched
snpEnrichment-package

~ Overview: SNPs enrichment analysis ~
compareEnrichment

Compare enrichment analysis between two SNPs list
initFiles

Initialize files for enrichment analysis
transcript-dataset

Transcript information in order to check the CIS status for SNPs
toyEnrichment-dataset

Toy dataset with SNP data