trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("trigger")
AuthorLin S. Chen <lchen@health.bsd.uchicago.edu>, Dipen P. Sangurdekar <dps@genomics.princeton.edu> and John D. Storey <jstorey@princeton.edu>
Bioconductor views GeneExpression GeneticVariability Genetics Microarray SNP
Date of publicationNone
MaintainerJohn D. Storey <jstorey@princeton.edu>
LicenseGPL-3
Version1.22.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/allFunctions.R
build
build/vignette.rds
data
data/datalist
data/yeast.rda
inst
inst/NEWS
inst/doc
inst/doc/trigger.R
inst/doc/trigger.Rnw
inst/doc/trigger.pdf
man
man/plot.Rd man/trigger-build.Rd man/trigger-class.Rd man/trigger-eigenR2.Rd man/trigger-export2cross.Rd man/trigger-link.Rd man/trigger-loclink.Rd man/trigger-mlink.Rd man/trigger-net.Rd man/trigger-netPlot2ps.Rd man/trigger-trait.Rd man/yeast.Rd
src
src/trigger.c
vignettes
vignettes/net50.pdf
vignettes/trigger.Rnw
vignettes/trigger.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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