Description Usage Arguments Details Value Note Author(s) References See Also Examples
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.
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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. |
Performs reports in the work directory.
It returns: Boxplot, Scatterplot, QQplot, Heatplot
Could be performed for QTL analysis in order to analyze the phenotypic data quality.
Lucia Gutierrez
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.
qtl.cross
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## 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)
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