traseR: GWAS trait-associated SNP enrichment analyses in genomic intervals
Version 1.6.0

traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.

Browse man pages Browse package API and functions Browse package files

AuthorLi Chen, Zhaohui S.Qin
Bioconductor views Alignment Coverage DataImport Genetics QualityControl Sequencing
Date of publicationNone
Maintainerli chen<li.chen@emory.edu>
LicenseGPL
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("traseR")

Man pages

CEU: Sampled SNPs from all SNPs of CEU population in 1000 genome...
plots: Visualize of trait-associated SNPs
print.traseR: Print the outcome of taSNP enrichment analyses
querys: Retrieve trait-associated SNPs based
taSNP: trait-associated SNPs in dbGaP and NHGRI downloaded from...
taSNPLD: linkage disequilibrium (>0.8) within 100kb SNPs of all...
Tcell: Peak regions of H3K4me1 in Peripheral blood T cell
traseR: TRait-Associated SNP EnRichment analyses
traseR-package: GWAS trait-associated SNP enrichment analyses in genomic...

Functions

CEU Man page
Tcell Man page
enrichTest Source code
plotContext Man page Source code
plotGene Man page Source code
plotInterval Man page Source code
plotPvalue Man page Source code
plotSNP Man page Source code
print.traseR Man page Source code
queryGene Man page Source code
queryKeyword Man page Source code
querySNP Man page Source code
taSNP Man page
taSNPLD Man page
traseR Man page Source code
traseR-package Man page

Files

DESCRIPTION
NAMESPACE
R
R/plots.R
R/querys.R
R/traseR.R
build
build/vignette.rds
data
data/CEU.RData
data/Tcell.RData
data/datalist
data/taSNP.RData
data/taSNPLD.RData
inst
inst/doc
inst/doc/traseR.R
inst/doc/traseR.Rnw
inst/doc/traseR.pdf
inst/unitTests
inst/unitTests/test_traseR.R
man
man/CEU.Rd
man/Tcell.Rd
man/plots.Rd
man/print.traseR.Rd
man/querys.Rd
man/taSNP.Rd
man/taSNPLD.Rd
man/traseR-package.Rd
man/traseR.Rd
tests
tests/runTests.R
vignettes
vignettes/traseR.Rnw
traseR documentation built on May 20, 2017, 10:44 p.m.