Stack QTL summary information into a super table

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Description

Stack QTL summary information into a super table ready for simple exporting

Usage

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qtlTable(..., intervalObj = NULL, labels = NULL, columns = "all")

Arguments

ldots

list of objects of class "wgaim". All "wgaim" models must have been analysed with the same genetic type (see wgaim.asreml)

intervalObj

a genetic object of class "interval" usually used in a wgaim fit

labels

a vector of character strings determining the trait names of each QTL table. if this is NULL then the trait names are found from the response of the wgaim model

columns

this can be either a numeric vector determining which columns of the QTL summaries should be outputted or "all" for all columns. The default is "all".

...

a numeric vector determining which columms of the summary should be returned (see Details)

Details

The super table is created by stacking the QTL summaries on top of each other using the models in ... from left to right. An extra column is created on the left hand side of the stacked table for the trait names given in the labels argument. The names are only placed in the first element of each table with NAs for the rest of the elements. This then allows simple exporting to spreadsheet packages or with the R/LaTeX package xtable.

Value

A data.frame object with stacked QTL summaries

Author(s)

Julian Taylor

References

Julian Taylor, Arunas Vebyla (2011). R Package wgaim: QTL Analysis in Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.

See Also

wgaim

Examples

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## Not run: 

## fit wgaim models

rktgw.qtl <- wgaim(rktgw.asf, phenoData = phenoRxK, intervalObj = genoRxK,
merge.by = "Genotype", trace = "trace.txt", na.method.X = "include")

rkyld.qtl <- wgaim(rkyld.asf, phenoData = phenoRxK, intervalObj = genoRxK,
merge.by = "Genotype", trace = "trace.txt", na.method.X = "include")

## create super table and export

qtlt <- qtlTable(rktgw.qtl, rkyld.qtl, labels = c("Conc.", "Shoot"))
print(xtable(qtlt), file = "superQTL.tex", include.rownames = FALSE)

## End(Not run)