pint (version 1.22.0)

summarize.region.parameters: Summarize overlapping models.

Description

Given a chromosomal region, summarize the model parameters from overlapping models. This heuristics gives a brief summary on average sample and probe effects within the region and aids interpretation. If multiple alteration profiles are detected within the region, the models are grouped and summarization is applied separately for each group containing overlapping models with high similarity.

Usage

summarize.region.parameters(region.genes, model, X, Y, grouping.th = 0.9, rm.na = TRUE)

Arguments

region.genes

A vector of gene names determining the investigated region.

model

Object of ChromosomeModels or GenomeModels class.

X

Data object. See help(screen.cgh.mrna). For instance, geneExp from our example data set.

Y

Data object. See help(screen.cgh.mrna). For instance, geneCopyNum from our example data set.

grouping.th

Similarity threshold for joining neighboring models.

rm.na

Remove genes with NA values from the output.

Value

z

Mean sample effects, averaged over the overlapping models for each sample.

W

Mean probe effects, averaged over the overlapping models for each probe. This is a list with elements X, Y, corresponding to the two data sets.

Details

Grouping of the models is based on heuristics where highly correlating models (>grouping.th) are merged. Will be improved later.

References

See citation("pint")

See Also

merge.top.regions

Examples

#  tmp <- summarize.region.parameters(top.region.genes, model, geneExp, geneCopyNum)
#  wx <- tmp$W$X
#  z <- tmp$z