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

Documentation for package ‘eqtl’ version 1.0

eqtl-package	Introductory comments on R/eqtl
A new starting point	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	Define QTL with support interval and exclusionary window
drop.peakfeat	Erase peak features in peak object
eqtlversion	Installed version of R/eqtl
First step	Importing the data
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	Resume 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