Description Usage Arguments Details Value Note Author(s) References See Also Examples
View source: R/diagnosis_functions.R
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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