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ctl (version 1.0.0-0)

Correlated Trait Locus (CTL) Mapping in R

Description

Analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL).

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Version

Install

install.packages('ctl')

Monthly Downloads

262

Version

1.0.0-0

License

GPL-3

Maintainer

Danny Arends

Last Published

September 20th, 2016

Functions in ctl (1.0.0-0)

ctl.circle

Circleplot CTL on multiple traits

basic.qc

Create quality control plots.

ath.result

Output of QCLscan after 5000 permutations on the metabolite expression data from Arabidopsis Thaliana.

image.CTLobject

Plot genome-wide CTL on multiple traits

ath.churchill

Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.

CTLhelper

CTLhelper - Helper functions for CTL mapping

hist.CTLobject

Plot histogram of CTL permutations

ctl-internal

Internal CTL functions

ctl-package

CTL - CTL mapping in experimental crosses

ath.metabolites

Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.

plot.CTLpermute

Differential correlation versus likelihood plotted in curves

ctl.lineplot

Lineplot CTL on multiple traits

CTLnetwork

CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits

print.CTLscan

Print the results of a single phenotype CTL scan

plot.CTLobject

Plot CTL curves or heatmaps

plot.CTLscan

Plot CTL results as bar, line or GWAS plot.

ctl.load

ctl.load - Load CTLs calculated by the D2.0 version

CTLprofiles

CTLprofiles - Extract CTL interaction profiles

print.CTLobject

Print the results of a CTL genome scan

CTLmapping

CTLmapping - Scan for correlated trait loci (CTL)

detect.peaks

detect.peaks - Peak detection algorithm to 'flatten' data above a certain threshold

scanSlopes.cross

scanSlopes.cross - Create a slope difference profile between two traits (R/qtl cross object)

scanSD

scanSD - Analyze the differences in Standard Deviation between genotypes between two traits

scanSD.cross

scanSD.cross - Analyze the differences in standard deviation between two traits at a certain genetic marker (R/qtl cross object)

CTLscan

CTLscan - Scan for Correlated Trait Locus (CTL)

qtlimage

Plot a QTL heatmap of the phenotypes scanned by CTLscan

CTLregions

CTLregions - Get all significant interactions from a genome-wide CTLscan

plotTraits

plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus

CTLsignificant

CTLsignificant - Get all significant interactions from a genome-wide CTLscan

CTLscan.cross

CTLscan.cross - Scan for Correlated Trait Locus (CTL) (R/qtl cross object)

scanSlopes

scanSlopes - Create a slope difference profile between two traits

yeast.brem

Example gene expression data from Saccharomyces cerevisiae on 301 RNA expressions.