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eqtl (version 1.1-7)
Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis
Description
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
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Version
1.1-7
1.1-6
1.1-5
1.1-4
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Install
install.packages('eqtl')
Monthly Downloads
53
Version
1.1-7
License
GPL (>= 2)
Maintainer
Ahmid A Khalili
Last Published
March 8th, 2012
Functions in eqtl (1.1-7)
Search functions
cim.peak
Genome scan using previously detected QTLs as covariates
map.peak
Summaries maximum LOD peak position from peak object
calc.Rsq
Estimate R square of individual QTLs and QTL interactions
classify.qtl
Estimate the acting type of expression QTL
BSpgmap
Genetic map data of a RIL population
cover.peak
List QTLs within a genetical region from a peak object
ATH.coord
Data on probes coordinates
drop.peakfeat
Erase peak features in peak object
seed10
Data on gene expression level variation
cleanphe
Remove undesired phenotypes and LOD results from cross and scanone object respectively
Importing the data
A simple way to import the data
peak.2.array
Build a simple array from a peak object
localize.qtl
Compute QTL physical positions from QTL genetic positions
A brief introduction
Introductory comments on R/eqtl
define.peak
Defines the QTL with support interval and exclusionary window
pseudo.map
The makers and pseudo-markers genetic map
mnames.map
List all markers from a cross object
gpt
Global Permutation Threshold
eqtlversion
Installed version of R/eqtl
Rsq.2.array
Add R square data to peak.array data frame
wash.covar
Erase additive covariates LOD peaks on the LOD curve
plotRsq
Plot R square data
peaksummary
Print summary of QTL definition
calc.adef
Compute the additive effect at each QTL marker
genoplot
Genome plot of the eQTL data on the expression traits locations