ATH.coord               Data on probes coordinates
BSpgmap                 Genetic map data of a RIL population
Importing the data      A simple way to import the data
Rsq.2.array             Add R square data to peak.array data frame
calc.Rsq                Estimate R square of individual QTLs and QTL
                        interactions
calc.adef               Compute the additive effect at each QTL marker
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 scanone object respectively
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
eqtl-package            Introductory comments on R/eqtl
eqtlversion             Installed version of R/eqtl
genoplot                Genome plot of the eQTL data on the expression
                        traits locations
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
seed10                  Data on gene expression level variation
wash.covar              Erase additive covariates LOD peaks on the LOD
                        curve
