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

## Documentation for package ‘eqtl’ version 1.1-7

- DESCRIPTION file.

## Help Pages

eqtl-package | Introductory comments on R/eqtl
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 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
eqtlversion | Installed version of R/eqtl
genoplot | Genome plot of the eQTL data on the expression traits locations
gpt | Global Permutation Threshold
Importing the data | A simple way to import the data
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