⚠️There's a newer version (1.0.0-10) of this package.Take me there.

ctl (version 1.0.0-2)

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).

Copy Link

Version

Install

install.packages('ctl')

Monthly Downloads

262

Version

1.0.0-2

License

GPL-3

Maintainer

Danny Arends

Last Published

August 3rd, 2018

Functions in ctl (1.0.0-2)

ctl.lineplot

Lineplot CTL on multiple traits

plot.CTLscan

Plot CTL results as bar, line or GWAS plot.

CTLscan.cross

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

CTLsignificant

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

ctl.load

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

print.CTLscan

Print the results of a single phenotype CTL scan

detect.peaks

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

yeast.brem

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

print.CTLobject

Print the results of a CTL genome scan

plotTraits

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

CTLprofiles

CTLprofiles - Extract CTL interaction profiles

plot.CTLpermute

Differential correlation versus likelihood plotted in curves

ath.metabolites

Example metabolite expression data from Arabidopsis Thaliana on 24 metabolites.

qtlimage

Plot a QTL heatmap of the phenotypes scanned by CTLscan

CTLmapping

CTLmapping - Scan for correlated trait loci (CTL)

QTLmapping

QTLmapping - QTL mapping method for CTL analysis

plot.CTLobject

Plot CTL curves or heatmaps

CTLnetwork

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

CTLregions

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

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)

scanSlopes

scanSlopes - Create a slope difference profile between two traits

scanSlopes.cross

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

ctl.circle

Circleplot CTL on multiple traits

basic.qc

Create quality control plots.

hist.CTLobject

Plot histogram of CTL permutations

CTLhelper

CTLhelper - Helper functions for CTL mapping

ctl-internal

Internal CTL functions

image.CTLobject

Plot genome-wide CTL on multiple traits

ath.result

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

ath.churchill

Example metabolite expression data from Arabidopsis Thaliana on 9 metabolites.

ctl-package

CTL - CTL mapping in experimental crosses