Implements classes and methods for large scale SNP enrichment analysis (e.g., SNPs associated with genes expression in a GWAS signal).
Not maintained anymore.
# Install snpEnrichment from CRAN:
install.packages("snpEnrichment")
# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("mcanouil/snpEnrichment")
Note: Internal data management in ‘snpEnrichment’ use RefSNP (rs) IDs.
library(snpEnrichment)
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
)
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
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
)
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
)
show(toyData)
print(toyData)
head(getEnrichSNP(toyData, type = "xSNP"))
show(toyData_exclude)
print(toyData_exclude)
head(getEnrichSNP(toyData_exclude, type = "eSNP"))
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.