summarizeInference: Summarize the inference results from from inferenceBGLR
In digiYozhik/msc_thesis: Functions to support master thesis

Description Usage Arguments Details Value Author(s) References Examples

Summarize the inference results from from inferenceBGLR

1	summarizeInference(P, obj)

`P`	a data frame that holds the design information and phenotypes for the data to be modeled. The data should hold following features, which are detailed below and represent the columns in the data frame. For inference on the thesis data set we use the data set P obtained by typing data(P) in the console.
`obj`	object obtained from the inferenceBGLR function.

The function summarizes the obtained results for the bias, MSPE, and predictive ability ("correlation") using the average across the different folds and replications as was specified in the cross-validation and inferenceBGLR function. Confidence intervals for the predictive ability were calculated using rho +/- 1.96*sqrt((1-rho^2)/(nrow(P)-2)). The confidence intervals for the bias and MSPE were calculated using a minimum and maximum value calculated as mean(metric) +/- SE(metric), following synbreed reporting by T. Albrecht in the summary.cvData function. See also reference.

A list of summarized inference measures from obj.

Ruud Derijcker

Wimmer, V., et al. (2012) synbreed: a framework for the analysis of genomic prediction data using R. Bioinformatics, 28: 2086-2087.

data(G)
data(P)
scheme <- crossValidate(x=P, id="GERMPLASM", factor="LOCATION", k=5,
                        replication=2, seed=NULL, exclusive=TRUE,
                        sampling="randomByID",verbose=TRUE)
output <- inferenceBGLR(P, CVscheme=scheme, modelName="modelG", id="GERMPLASM",
                       G=G, factor="LOCATION", trait="YIELD", nIter=1500, burnIn=250,
                       replications=2)
output <- summarizeInference(P, output)
output