qtlTable: Stack QTL summary information into a super table

In wgaim: Whole Genome Average Interval Mapping for QTL Detection and Estimation using ASReml-R

Description

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

Usage

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

Arguments

...	list of objects of class "wgaim". All models must have been analysed with the same gen.type (see help for wgaim.asreml()).
intervalObj	a genetic object of class "interval" reequire in a wgaim analysis (see help for wgaim.asreml()). This is required to be non NULL
labels	a vector of character strings describing the trait names of each model QTL table.
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".

Details

The super table is created by obtaining the QTL summaries for each model in ... using summary.wgaim() and then row binding them together. An extra column is created on the left hand side of the super table for the trait names given in the labels argument. If labels = NULL then trait names are extracted from the left hand-side of the fixed component of the associated wgaim model. The returned super table allows simple exporting to spreadsheet software 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

## Not run: 

## fit wgaim models

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

rkyld.qtl <- wgaim(rkyld.asf, intervalObj = genoRxK, merge.by = "Genotype",
                   trace = "trace.txt", na.action = 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)

wgaim documentation built on Oct. 3, 2019, 9:03 a.m.