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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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README.md

SNPs Enrichment Analysis With Sampling

Lifecycle: retired GitHub tag Travis-CI Build Status AppVeyor Build Status Coverage Status (codecov) CRAN_Status_Badge cran checks_worst CRAN_Download_total

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

Not maintained anymore.

Installation

# Install snpEnrichment from CRAN:
install.packages("snpEnrichment")

# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("mcanouil/snpEnrichment")

Overview

Note: Internal data management in ‘snpEnrichment’ use RefSNP (rs) IDs.

Load snpEnrichment

library(snpEnrichment)

Prepare data

snpInfoDir <- system.file("extdata/snpInfo", package = "snpEnrichment")
signalFile <- system.file("extdata/Signal/toySignal.txt", package = "snpEnrichment")

initFiles(pattern = "Chrom", snpInfoDir, signalFile, mc.cores = 1)

writeLD(
  pattern = "Chrom", 
  snpInfoDir, 
  signalFile, 
  ldDir = NULL,
  ldThresh = 0.8, 
  depth = 1000, 
  mc.cores = 1
)

Read data

snpListDir <- system.file("extdata/List", package = "snpEnrichment")
data(transcript)
transcriptFile <- transcript

toyData <- readEnrichment(
    pattern = "Chrom", 
    signalFile, 
    transcriptFile,
    snpListDir, 
    snpInfoDir,
    distThresh = 1000, 
    sigThresh = 0.05, 
    LD = TRUE, 
    ldDir = NULL,
    mc.cores = 1
)
toyData

Compute results

reSample(
  object = toyData,
  nSample = 10,
  empiricPvalue = TRUE,
  MAFpool = c(0.05, 0.10, 0.2, 0.3, 0.4, 0.5),
  mc.cores = 1,
  onlyGenome = TRUE
)

5. Further analysis: Exclude SNP from original list.

excludeFile <- c(
  "rs4376885", "rs17690928", "rs6460708", "rs13061537", "rs11769827",
  "rs12717054", "rs2907627", "rs1380109", "rs7024214", "rs7711972",
  "rs9658282", "rs11750720", "rs1793268", "rs774568", "rs6921786",
  "rs1699031", "rs6994771", "rs16926670", "rs465612", "rs3012084",
  "rs354850", "rs12803455", "rs13384873", "rs4364668", "rs8181047",
  "rs2179993", "rs12049335", "rs6079926", "rs2175144", "rs11564427",
  "rs7786389", "rs7005565", "rs17423335", "rs12474102", "rs191314",
  "rs10513168", "rs1711437", "rs1992620", "rs283115", "rs10754563",
  "rs10851727", "rs2173191", "rs7661353", "rs1342113", "rs7042073",
  "rs1567445", "rs10120375", "rs550060", "rs3761218", "rs4512977"
)

# or
excludeFile <- system.file("extdata/Exclude/toyExclude.txt", package = "snpEnrichment")
toyData_exclude <- excludeSNP(toyData, excludeFile, mc.cores = 1)

Warning: compareEnrichment is in development!!

compareResults <- compareEnrichment(
  object.x = toyData,
  object.y = toyData_exclude,
  pattern = "Chrom",
  nSample = 10,
  empiricPvalue = TRUE,
  mc.cores = 1,
  onlyGenome = TRUE
)

Watch results

show(toyData)
print(toyData)
head(getEnrichSNP(toyData, type = "xSNP"))

show(toyData_exclude)
print(toyData_exclude)
head(getEnrichSNP(toyData_exclude, type = "eSNP"))

Getting help

If you encounter a clear bug, please file a minimal reproducible example on github. For questions and other discussion, please contact the package maintainer.


Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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