trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

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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@health.bsd.uchicago.edu>, Dipen P. Sangurdekar <dps@genomics.princeton.edu> and John D. Storey <jstorey@princeton.edu>
Date of publication
None
Maintainer
John D. Storey <jstorey@princeton.edu>
License
GPL-3
Version
1.20.0

View on Bioconductor

Man pages

plot
Graphical Display of Trigger Analysis
trigger-build
Format the input data and create an Trigger object
trigger-class
A class to store and analyze data for Transcriptional...
trigger-eigenR2
Estimate the proportion of genome-wide variation explained by...
trigger-export2cross
Export Trigger data to R/qtl's cross class object
trigger-link
Genomewide eQTL analysis
trigger-loclink
Estimate local-linkage probability for each gene
trigger-mlink
Multi-Locus Linkage (Epistasis) Analysis
trigger-net
Network-Trigger analysis
trigger-netPlot2ps
Write the network from a trigger probability matrix to a...
trigger-trait
Trait-trigger analysis
yeast
A yeast data set for Transcriptional Regulation Inference...

Files in this package

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