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

Install

install.packages('eqtl')

Monthly Downloads

Version

1.1-7

License

GPL (>= 2)

Maintainer

Ahmid A Khalili

Last Published

March 8th, 2012

Functions in eqtl (1.1-7)

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