FUNLDA (version 1.1)

FitLDAModelNewTissues: Update the tissues in a fitted LDA model

Description

Update the tissues in a fitted LDA model

Usage

FitLDAModelNewTissues(newtissue.data, summary.c, inner.iters = 200)

Arguments

newtissue.data

A data frame with character-valued columns rs and cat and numeric-valued columns with annotations. Each row contains data for one SNP in one tissue rs is an ID for the SNP, which need not be unique, and cat is an ID for each tissue, which must match an ID for which training data was included when fitting the LDA model. Annotation columns must have column names matching those supplied when fitting the LDA model.

summary.c

A fitted LDA model created using FitLDAModel or FitLDAModelNewTissues.

inner.iters

Integer specifying number of inner iterations

Value

a fitted LDA model, as returned by FitLDAModel, that can be used with Predict for the tissues in newtissue.data

Examples

# NOT RUN {
  data(training)
  summary.c <- FitLDAModel(training.data=training, nclust=3,
                         kde.nbins=100, iters=50, inner.iters=50)
  data(tissuenew)
  newtissues <- FitLDAModelNewTissues(newtissue.data=tissuenew,
                                     summary.c=summary.c,
                                     inner.iters=50)
# }