join.top.regions: Merge the overlapping top chromosomal regions.

In pint: Pairwise INTegration of functional genomics data

Description

Select the top models that exceed the threshold and merge the overlapping windows. Useful for interpreting the results.

Usage

join.top.regions(model, feature.info, quantile.th = 0.95, augment = FALSE)

Arguments

model	Object of ChromosomeModels or GenomeModels class.
feature.info	A data frame containing annotations for genes. For instance the geneExp$info table from our example data set (see data(chromosome17)).
quantile.th	Threshold to define what quantile of the genes to include in the top region list, based on dependency scores for each gene.
augment	If TRUE, list also genes that were not used for modeling but available in the annotations (feature.info) and residing within the same region.

Value

A list; each element is a vector of gene names that correspond to one continuous region.

Author(s)

Leo Lahti [e-mail]

References

See citation("pint")

See Also

summarize.region.parameters

Examples

## NOT RUN
# top.regions <- join.top.regions(model, geneExp$info, quantile.th = 0.95)

pint documentation built on Oct. 31, 2019, 2:41 a.m.