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mppR

Multi-Parent Population QTL Analysis

Analysis of experimental multi-parent populations to detect regions of the genome (called quantitative trait loci, QTLs) influencing phenotypic traits. The population must be composed of crosses between a set of at least three parents (e.g. factorial design, 'diallel', or nested association mapping). The functions cover data processing, QTL detection, and results visualization. The implemented methodology is described by Garin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017) <doi:10.1007/s00122-017-2923-3>.

Functions (33)

CV_partition

Cross validation partition

IBD.mppData

IBD coding for mppData objects

IBS.mppData

IBS coding for mppData objects

Multi-QTL effect MPP analysis

Quality control for mppData objects

QTL global and partial R squared

QTL_gen_effects

QTL genetic effects

QTL_pred_R2

Predicted QTL global and partial R squared

QTL candidates selection

Reduced genotype data maize US-NAM population

Reduced map maize US-NAM population

USNAM_pheno

Reduced phenotype data from Maize US-NAM population

create.mppData

Create a multi-parent population data object

design_connectivity

Connected parts of a MPP design

inc_mat_QTL

QTL incidence matrix

Complete mppData object

mppData_init

mppData object with raw data

MPP Composite Interval Mapping

MPP cross-validation

MPP Simple Interval Mapping

mpp_back_elim

Backward elimination on QTL candidates

QTL significance threshold by permutation

MPP QTL analysis

Parental clustering

parent_cluster.mppData

Parent clustering for mppData objects

plot.QTLprof

plot QTL profile

print.summary.QR2Res

Print summary.QR2Res object

print.summary.QeffRes

Print summary.QeffRes object

print.summary.mppData

Print summary.mppData object

subset.mppData

Subset mppData object

summary.QR2Res

Summary of QR2Res object

summary.QeffRes

Summary of QeffRes object

summary.mppData

Summary of mppData object

mppR

Multi-Parent Population QTL Analysis

v1.2.1

GPL-3

Authors

Vincent Garin [aut, cre], Valentin Wimmer [aut], Dietrich Borchardt [ctb, dtc], Fred van Eeuwijk [ctb, ths], Marcos Malosetti [ctb, ths]

Initial release

2020-02-10

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