eqtl: Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis

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Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.

Author
Ahmid A. Khalili and Olivier Loudet
Date of publication
2012-03-08 07:00:00
Maintainer
Ahmid A. Khalili <hamid.khalili@gmail.com>
License
GPL (>= 2)
Version
1.1-7

View on CRAN

Man pages

AA.brief.introduction
Introductory comments on R/eqtl
A.importing.data
A simple way to import the data
ATH.coord
Data on probes coordinates
BSpgmap
Genetic map data of a RIL population
calc.adef
Compute the additive effect at each QTL marker
calc.Rsq
Estimate R square of individual QTLs and QTL interactions
cim.peak
Genome scan using previously detected QTLs as covariates
classify.qtl
Estimate the acting type of expression QTL
cleanphe
Remove undesired phenotypes and LOD results from cross and...
cover.peak
List QTLs within a genetical region from a peak object
define.peak
Defines the QTL with support interval and exclusionary window
drop.peakfeat
Erase peak features in peak object
eqtlversion
Installed version of R/eqtl
genoplot
Genome plot of the eQTL data on the expression traits...
gpt
Global Permutation Threshold
localize.qtl
Compute QTL physical positions from QTL genetic positions
map.peak
Summaries maximum LOD peak position from peak object
mnames.map
List all markers from a cross object
peak.2.array
Build a simple array from a peak object
peaksummary
Print summary of QTL definition
plotRsq
Plot R square data
pseudo.map
The makers and pseudo-markers genetic map
Rsq.2.array
Add R square data to peak.array data frame
seed10
Data on gene expression level variation
wash.covar
Erase additive covariates LOD peaks on the LOD curve

Files in this package

eqtl
eqtl/MD5
eqtl/status.txt
eqtl/R
eqtl/R/wash.covar.R
eqtl/R/Rsq.2.array.R
eqtl/R/pseudo.map.R
eqtl/R/plotRsq.R
eqtl/R/peaksummary.R
eqtl/R/peak.2.array.R
eqtl/R/mnames.map.R
eqtl/R/map.peak.R
eqtl/R/localize.qtl.R
eqtl/R/gpt.R
eqtl/R/genoplot.R
eqtl/R/eqtlversion.R
eqtl/R/drop.peakfeat.R
eqtl/R/define.peak.R
eqtl/R/cover.peak.R
eqtl/R/cleanphe.r
eqtl/R/classify.qtl.R
eqtl/R/cim.peak.R
eqtl/R/calc.Rsq.R
eqtl/R/calc.adef.R
eqtl/NAMESPACE
eqtl/man
eqtl/man/wash.covar.Rd
eqtl/man/seed10.Rd
eqtl/man/Rsq.2.array.Rd
eqtl/man/pseudo.map.Rd
eqtl/man/plotRsq.Rd
eqtl/man/peaksummary.Rd
eqtl/man/peak.2.array.Rd
eqtl/man/mnames.map.Rd
eqtl/man/map.peak.Rd
eqtl/man/localize.qtl.Rd
eqtl/man/gpt.Rd
eqtl/man/genoplot.Rd
eqtl/man/eqtlversion.Rd
eqtl/man/drop.peakfeat.Rd
eqtl/man/define.peak.Rd
eqtl/man/cover.peak.Rd
eqtl/man/cleanphe.Rd
eqtl/man/classify.qtl.Rd
eqtl/man/cim.peak.Rd
eqtl/man/calc.Rsq.Rd
eqtl/man/calc.adef.Rd
eqtl/man/BSpgmap.Rd
eqtl/man/ATH.coord.Rd
eqtl/man/AA.brief.introduction.Rd
eqtl/man/A.importing.data.Rd
eqtl/license.txt
eqtl/docs
eqtl/docs/eQTLmanual_270410.pdf
eqtl/DESCRIPTION
eqtl/data
eqtl/data/seed10.rda
eqtl/data/datalist
eqtl/data/BSpgmap.rda
eqtl/data/ATH.coord.rda