trigger

Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Bioconductor version: Development (3.0)

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.

Author: Lin S. Chen <lchen at health.bsd.uchicago.edu>, Dipen P. Sangurdekar <dps at genomics.princeton.edu> and John D. Storey <jstorey at princeton.edu>

Maintainer: John D. Storey <jstorey at princeton.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("trigger")

To cite this package in a publication, start R and enter:

    citation("trigger")

Documentation

PDF R Script Trigger Tutorial
PDF   Reference Manual

Details

biocViews GeneExpression, GeneticVariability, Genetics, Microarray, SNP, Software
Version 1.11.0
In Bioconductor since BioC 2.9 (R-2.14)
License GPL-3
Depends R (>= 2.14.0), corpcor, qtl
Imports qvalue, methods, graphics, sva
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Package Downloads

Package Source trigger_1.11.0.tar.gz
Windows Binary trigger_1.11.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) trigger_1.11.0.tgz
Mac OS X 10.9 (Mavericks)
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