Package: trigger 1.51.0

John D. Storey

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.

Authors:Lin S. Chen <[email protected]>, Dipen P. Sangurdekar <[email protected]> and John D. Storey <[email protected]>

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trigger.pdf |trigger.html✨
trigger/json (API)
NEWS

# Install 'trigger' in R:
install.packages('trigger', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • yeast - A yeast data set for Transcriptional Regulation Inference from Genetics of Gene ExpRession

On BioConductor:trigger-1.51.0(bioc 3.20)trigger-1.50.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

10 exports 0.82 score 87 dependencies

Last updated 2 months agofrom:eca1cb47d9

Exports:plottrigger.buildtrigger.eigenR2trigger.export2crosstrigger.linktrigger.loclinktrigger.mlinktrigger.nettrigger.netPlot2pstrigger.trait

Dependencies:annotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecorpcorcpp11crayoncurlDBIedgeRfansifarverfastmapformatRfutile.loggerfutile.optionsgenefilterGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngqtlqvalueR6RColorBrewerRcppreshape2rlangRSQLiteS4VectorsscalessnowstatmodstringistringrsurvivalsvasystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectorzlibbioc

Trigger Tutorial

Rendered fromtrigger.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Graphical Display of Trigger Analysisplot plot,trigger,missing-method
A class to store and analyze data for Transcriptional Regulation Inference from Genetics of Gene ExpRessiontrigger-class
Format the input data and create an Trigger objecttrigger.build
Estimate the proportion of genome-wide variation explained by each eQTLtrigger.eigenR2 trigger.eigenR2,trigger-method
Export Trigger data to R/qtl's cross class objecttrigger.export2cross trigger.export2cross,trigger-method
Genomewide eQTL analysistrigger.link trigger.link,trigger-method
Estimate local-linkage probability for each genetrigger.loclink trigger.loclink,trigger-method
Multi-Locus Linkage (Epistasis) AnalysisMultiple-locus linkage trigger.mlink trigger.mlink,trigger-method
Network-Trigger analysistrigger.net trigger.net,trigger-method
Write the network from a trigger probability matrix to a postscript filetrigger.netPlot2ps trigger.netPlot2ps,trigger-method
Trait-trigger analysistrigger.trait trigger.trait,trigger-method
A yeast data set for Transcriptional Regulation Inference from Genetics of Gene ExpRessionyeast