eqtl: Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis
Version 1.1-7

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

Browse man pages Browse package API and functions Browse package files

AuthorAhmid A. Khalili and Olivier Loudet
Date of publication2012-03-08 07:00:00
MaintainerAhmid A. Khalili <hamid.khalili@gmail.com>
LicenseGPL (>= 2)
Version1.1-7
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("eqtl")

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

Functions

ATH.coord Man page
BSpgmap Man page
Importing the data Man page
Rsq.2.array Man page
calc.Rsq Man page Source code
calc.adef Man page
cim.peak Man page
classify.qtl Man page Source code
cleanphe Man page
cover.peak Man page
define.peak Man page
drop.peakfeat Man page
eqtl-package Man page
eqtlversion Man page Source code
genoplot Man page Source code
gpt Man page
localize.qtl Man page
map.peak Man page
mnames.map Man page
peak.2.array Man page
peaksummary Man page
plotRsq Man page
pseudo.map Man page
seed10 Man page
wash.covar Man page

Files

MD5
status.txt
R
R/wash.covar.R
R/Rsq.2.array.R
R/pseudo.map.R
R/plotRsq.R
R/peaksummary.R
R/peak.2.array.R
R/mnames.map.R
R/map.peak.R
R/localize.qtl.R
R/gpt.R
R/genoplot.R
R/eqtlversion.R
R/drop.peakfeat.R
R/define.peak.R
R/cover.peak.R
R/cleanphe.r
R/classify.qtl.R
R/cim.peak.R
R/calc.Rsq.R
R/calc.adef.R
NAMESPACE
man
man/wash.covar.Rd
man/seed10.Rd
man/Rsq.2.array.Rd
man/pseudo.map.Rd
man/plotRsq.Rd
man/peaksummary.Rd
man/peak.2.array.Rd
man/mnames.map.Rd
man/map.peak.Rd
man/localize.qtl.Rd
man/gpt.Rd
man/genoplot.Rd
man/eqtlversion.Rd
man/drop.peakfeat.Rd
man/define.peak.Rd
man/cover.peak.Rd
man/cleanphe.Rd
man/classify.qtl.Rd
man/cim.peak.Rd
man/calc.Rsq.Rd
man/calc.adef.Rd
man/BSpgmap.Rd
man/ATH.coord.Rd
man/AA.brief.introduction.Rd
man/A.importing.data.Rd
license.txt
docs
docs/eQTLmanual_270410.pdf
DESCRIPTION
data
data/seed10.rda
data/datalist
data/BSpgmap.rda
data/ATH.coord.rda
eqtl documentation built on May 19, 2017, 4:34 p.m.