enrichment.feat: Enrichment of features with respect to annotation types
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Note Author(s)

Enrichment of features with respect to annotation types

1	enrichment.feat(x, annotations, region.bounds)

`x`	An object of type `feat`
`annotations`	An object of type `feat` containing some annotations.
`region.bounds`	An object of type `feat` representing the boundary coordinates of the regions of interest (such as chromosome boundaries). All elements from the first two arguments should fall entirely within region.bounds.

A data frame with two columns and a row for each type of element in the annotations. The second column gives the fold-enrichment of x across the corresponding annotation type, which is equal to the fraction of x which fall within the annotation type, divided by the fraction of the entire region covered by the annotation type.

If any of the arguments to this function are passed as pointers to objects stored in C, they will be sorted after this function call.

Melissa J. Hubisz

rphast documentation built on May 1, 2019, 9:26 p.m.