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.
1 2 3 4 5 6 7 8 9 10 | 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
|
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