R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
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Results 1 - 10 of 12 found.
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mpMap : Multi-parent RIL genetic analysis

Package: mpMap
Type: Package
Title: Multi-parent RIL genetic analysis
Version: 1.14
Date: 2012-06-06
Author: Emma Huang
Maintainer: Emma Huang <Emma.Huang@csiro.au>
Description: Tools for constructing linkage maps, reconstructing
haplotypes, estimating linkage disequilibrium and QTL mapping
in multi-parent RIL designs (e.g. MAGIC)
License: GPL-2
LazyLoad: yes
Depends: gdata, seriation, qtl, wgaim
Suggests: aod, asreml, happy.hbrem, Heatplus, MASS, VPdtw, lattice
Collate: 'add3pt.R' 'calc.genoprob2.R' 'calcmpprob.R' 'check-ped.R'
'check-QTL.R' 'clean.mpcross.R' 'cleanmap.R' 'cleanrf.R'
'combine-chr.R' 'combine-ibd.R' 'combine-ld.R' 'combine-rf.R'
'compare-orders.R' 'compute-bnld.R' 'compute-bnrf.R'
'computemap.R' 'convertped.R' 'CR-calcLD.R' 'CR-cross.R'
'CR-estrf.R' 'CR-gen-geno.R' 'fill.R' 'fillmiss.R' 'findqtl2.R'
'fit.mpqtl.R' 'gen4ped.R' 'gen8ped.R' 'generate-error.R'
'generate-obs.R' 'generate-pheno.R' 'getpval.R' 'mapcomp.R'
'maporder.R' 'mp-mapdist.R' 'mpadd.R' 'mpcalcld.R' 'mpcross.R'
'mpestrf.R' 'mpgroup.R' 'mpIM.R' 'mpMap-output.R' 'mporder.R'
'mpprob.R' 'mpsegrat.R' 'nai.R' 'plot.mpcross.R'
'plot.mpprob.R' 'plot.mpqtl.R' 'plotlink.map.R'
'print.mapcomp.R' 'print.mpcross.R' 'print.mpprob.R'
'print.mpqtl.R' 'qtlmap.R' 'read.mpcross.R'
'reorgRIgenoprob2.R' 'sim.mpcross.R' 'sim.mpped.R'
'sim.sigthr.R' 'subset.mpcross.R' 'subset.mpprob.R'
'summary.mpcross.R' 'summary.mpprob.R' 'summary.mpqtl.R'
'supportinterval.R' 'waldTests.R'
Packaged: 2012-06-06 04:42:08 UTC; hua032
Repository: CRAN
Date/Publication: 2012-06-06 05:59:03

● Data Source: CranContrib
● 0 images, 38 functions, 0 datasets
● Reverse Depends: 0

mQTL : Metabolomic Quantitative Trait Locus Mapping

Package: mQTL
Type: Package
Title: Metabolomic Quantitative Trait Locus Mapping
Version: 1.0
Date: 2013-09-18
Author: Lyamine Hedjazi and Jean-Baptiste Cazier
Maintainer: Lyamine Hedjazi <l.hedjazi@fondation-ican.com>
Description: mQTL provides a complete QTL analysis pipeline for metabolomic data.
Distinctive features include normalisation using PQN approach, peak alignment
using RSPA approach, dimensionality reduction using SRV approach and finally
QTL mapping using R/qtl package.
License: GPL
LazyLoad: yes
LazyData: yes
NeedsCompilation: yes
Repository: CRAN
Depends: R (>= 2.15.0), qtl, MASS, outliers
Packaged: 2013-10-21 09:31:01 UTC; Utilisateur
Date/Publication: 2013-10-21 12:44:23

● Data Source: CranContrib
● 0 images, 20 functions, 0 datasets
● Reverse Depends: 0

dlmap : Detection Localization Mapping for QTL

Package: dlmap
Type: Package
Title: Detection Localization Mapping for QTL
Version: 1.13
Date: 2012-08-09
Author: Emma Huang and Andrew George
Maintainer: Emma Huang <Emma.Huang@csiro.au>
Description: QTL mapping in a mixed model framework with separate
detection and localization stages. The first stage detects the
number of QTL on each chromosome based on the genetic variation
due to grouped markers on the chromosome; the second stage uses
this information to determine the most likely QTL positions.
The mixed model can accommodate general fixed and random
effects, including spatial effects in field trials and pedigree
effects. Applicable to backcrosses, doubled haploids,
recombinant inbred lines, F2 intercrosses, and association
mapping populations.
License: GPL-2
Depends: qtl, ibdreg, wgaim, nlme, mgcv
Suggests: asreml
Collate: 'calc.genoprob2.R' 'calcpos.R' 'cintern.R' 'dlcross.cross.R'
'dlcross.dlmap.R' 'dlcross.other.R' 'dlcross.R' 'dldetect.R'
'dllocalize.R' 'dlmap.R' 'dlmapdet.R' 'dlmaploc.R' 'dltest.R'
'ngen.dlcross.R' 'ngen.dlmap.R' 'ngen.R' 'nmrk.dlcross.R'
'nmrk.dlmap.R' 'nmrk.R' 'nphen.dlcross.R' 'nphen.dlmap.R'
'nphen.R' 'plot.dlcross.R' 'plot.dlmap.R' 'print.dlcross.R'
'print.dlmap.R' 'profileplot.dlmap.R' 'profileplot.R' 'pvfx.R'
'qchibar.R' 'summary.dlcross.R' 'summary.dlmap.R'
'waldtest.asreml.R' 'waldtest.R'
Packaged: 2012-08-09 05:34:15 UTC; hua032
Repository: CRAN
Date/Publication: 2012-08-09 05:48:27

● Data Source: CranContrib
● Cran Task View: Genetics
● 0 images, 5 functions, 2 datasets
● Reverse Depends: 0

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

Package: eqtl
Type: Package
Title: Tools for analyzing eQTL experiments: A complementary to Karl
Broman's 'qtl' package for genome-wide analysis
Version: 1.1-7
Date: 2012-3-6
Author: Ahmid A. Khalili and Olivier Loudet
Maintainer: Ahmid A. Khalili <hamid.khalili@gmail.com>
Contributors: Jennifer Yansouni, Karl Broman
Depends: R (>= 2.10), qtl (>= 1.7.12)
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
License: GPL (>= 2)
Packaged: 2012-03-06 20:09:28 UTC; kbroman
Repository: CRAN
Date/Publication: 2012-03-08 07:00:00

● Data Source: CranContrib
● 0 images, 22 functions, 3 datasets
● Reverse Depends: 0

ASMap : Linkage Map Construction using the MSTmap Algorithm

Package: ASMap
Type: Package
Title: Linkage Map Construction using the MSTmap Algorithm
Version: 0.4-7
Date: 2016-06-24
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler
<david.butler@daff.qld.gov.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Suggests: knitr
VignetteBuilder: knitr
Depends: R (>= 2.10), qtl, gtools, fields, RColorBrewer, lattice
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2016-06-24 04:44:58 UTC; julian.taylor
Repository: CRAN
Date/Publication: 2016-06-24 09:53:21

● Data Source: CranContrib
● 4 images, 20 functions, 5 datasets
● Reverse Depends: 0

vqtl : Genome Scans to Accommodate and Target Genetic and Non-Genetic Effects on Trait Variance

Package: vqtl
Type: Package
Title: Genome Scans to Accommodate and Target Genetic and Non-Genetic
Effects on Trait Variance
Version: 1.0
Date: 2016-03-04
Author: Robert Corty
Maintainer: Robert Corty <rcorty@gmail.com>
Description: In recognition that there are many factors (genetic loci, macro-genetic factors such as sex,
and environmental factors) that influence the environmental variation, the 'vqtl' package conducts genome
scans that accommodate and target these factors. The main functions of this package, scanonevar() and
scanonevar.perm() take as input a cross object from the popular 'qtl' package.
Depends: R (>= 2.14.0), dglm, evd, dplyr, qtl
Imports: RColorBrewer, gtools, stringr, plyr, scales, graphics,
grDevices
License: GPL-3
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-03-06 18:47:06 UTC; rcorty
Repository: CRAN
Date/Publication: 2016-03-07 01:01:40

● Data Source: CranContrib
● 0 images, 18 functions, 0 datasets
● Reverse Depends: 0

wgaim : Whole Genome Average Interval Mapping for QTL Detection using Mixed Models

Package: wgaim
Type: Package
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Version: 1.4-10
Date: 2015-06-026
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, Simon Diffey <simon.diffey@dpi.nsw.gov.au>, Ari Verbyla <ari.verbyla@csiro.au> and Brian Cullis <bcullis@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Depends: R (>= 2.0.0), qtl, lattice
SystemRequirements: asreml-R 3.x
Description: Integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-06-26 02:21:41 UTC; julian.taylor
Repository: CRAN
Date/Publication: 2015-06-26 10:55:21

● Data Source: CranContrib
● Cran Task View: Genetics
● 0 images, 11 functions, 6 datasets
● Reverse Depends: 2

pheno2geno : High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

Package: pheno2geno
Version: 1.3.1
Date: 2015-03-25
Title: High-Throughput Generation of Genetic Markers and Maps from
Molecular Phenotypes for Crosses Between Inbred Strains
Author: Konrad Zych <k.zych@rug.nl> and Danny Arends <danny.arends@gmail.com>
Maintainer: Konrad Zych <k.zych@rug.nl>
Description: High-throughput generation of genetic markers from molecular phenotypes for crosses between inbred strains. These markers can be use to saturate existing genetic map or creating a new one.
Depends: R (>= 2.14.1), graphics, stats, utils, qtl, VGAM, mixtools
Suggests: RankProd
License: GPL-3
NeedsCompilation: no
Packaged: 2015-03-25 12:07:31 UTC; Konrad
Repository: CRAN
Date/Publication: 2015-03-25 16:08:51

● Data Source: CranContrib
● 0 images, 31 functions, 2 datasets
● Reverse Depends: 0

qtlbook : Datasets for the R/qtl Book

Package: qtlbook
Version: 0.18-5
Date: 2016-05-21
Title: Datasets for the R/qtl Book
Author: Karl W Broman <kbroman@biostat.wisc.edu>
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Description: Datasets for the book, A Guide to QTL Mapping with R/qtl.
Depends: R (>= 2.10.1), qtl
License: GPL-3
URL: http://www.rqtl.org/book
NeedsCompilation: no
Packaged: 2016-05-21 13:13:39 UTC; kbroman
Repository: CRAN
Date/Publication: 2016-05-22 09:21:02

● Data Source: CranContrib
● 0 images, 0 functions, 9 datasets
● Reverse Depends: 0

qtlhot : Inference for QTL Hotspots

Package: qtlhot
Version: 0.9.0
Date: 2013-09-18
Author: Elias Chaibub Neto <echaibub@hotmail.com> and Brian S Yandell <byandell@wisc.edu>
Title: Inference for QTL Hotspots
Description: Functions to infer co-mapping trait hotspots and causal models
Maintainer: Brian S. Yandell <byandell@wisc.edu>
Depends: R (>= 2.10), stats, qtl, lattice, corpcor, mnormt
LazyLoad: yes
LazyData: yes
License: GPL (>= 2)
URL: http://www.stat.wisc.edu/~yandell/statgen
Packaged: 2013-09-18 18:17:25 UTC; yandell
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-09-19 08:54:03

● Data Source: CranContrib
● 0 images, 13 functions, 0 datasets
● Reverse Depends: 0