pq.diagnostics: Performs phenotypic data quality diagnostics.

In lmem.qtler: Linear Mixed Effects Models for QTL Mapping for Multienvironment and Multitrait Analysis

Description

Performs phenotypic data quality diagnostic of an object of class cross created by the qtl.cross function, including summary descriptive diagnostics, correlation across traits,and distribution of traits.

Usage

pq.diagnostics (crossobj, boxplot = TRUE, qqplot = FALSE,
scatterplot = TRUE,heatplot = TRUE)

Arguments

crossobj	An object of class = cross obtained from the qtl.cross function from this package, or the read.cross function from r/qtl package (Broman and Sen, 2009). This file contains phenotypic means, genotypic marker score, and genetic map.
boxplot	Indicates whether a boxplot should be performed. TRUE/FALSE term. TRUE is set as default.
qqplot	Indicates whether a qqplot should be performed. TRUE/FALSE term. FALSE is set as default.
scatterplot	Indicates whether a scatterplot should be performed. TRUE/FALSE term. TRUE is set as default.
heatplot	Indicates whether a phenotypic heatplot should be performed. TRUE is set as default.

Details

Performs reports in the work directory.

Value

It returns: Boxplot, Scatterplot, QQplot, Heatplot

Note

Could be performed for QTL analysis in order to analyze the phenotypic data quality.

Author(s)

Lucia Gutierrez

References

Broman KW, Sen S (2009) A Guide to QTL Mapping with R/qtl. Springer, NewYork. Comadran J, Thomas W, van Eeuwijk F, Ceccarelli S, Grando S, Stanca A, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett C, Russell J (2009) Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119:175-187 Milne et al., (2010) Flapjack - graphical genotype visualization. Bioinformatics 26(24), 3133-3134.

See Also

qtl.cross

Examples

## Not run: 
data (SxM_geno)
data (SxM_map)
data (SxM_pheno)

P.data <- SxM_pheno
G.data <- SxM_geno
map.data <- SxM_map

cross.data <- qtl.cross (P.data, G.data, map.data,
cross='dh', heterozygotes = FALSE)

summary (cross.data)
jittermap (cross.data)

Pheno Quality
pq.diagnostics (crossobj=cross.data)

## End(Not run)

lmem.qtler documentation built on May 2, 2019, 1:46 p.m.