break.annot-class: Class to store breakpoint annotations in association with...

Description Arguments Value

Description

Class to store breakpoint annotations in association with genomic features (e.g. gene loci)

Arguments

input

(data.frame): the breakpoint info containing data.frame, this will be occupied by the CNV segmentation data in the case of cnv.break.annot or SV for sv.break.annot. Unique random string rownames are added to the provided data.frame.

genesgr

(GRanges): a GRanges object with genomic features (e.g. genes) to which breakpoints are mapped

disruptSamples

(list): a list which names correspond to genomic features and values correspond to sample ids harboring breakpoints overlapping with said features

disruptBreaks

(list): a list which names correspond to genomic features and values correspond to the ids of breakpount mapped onto them. Break ids are linked to the 'input' data.frame rownames

upstreamSamples

(list): a list which names correspond to genomic features and values correspond to sample ids harboring breakpoints overlapping with upstream region of said features

upstreamBreaks

(list): a list which names correspond to genomic features and values correspond to the ids of breakpount mapped onto upstream regions Break ids are linked to the 'input' data.frame rownames

param

(list): a list of parametres provided for the annotation function

Value

an instance of the class 'break.annot' containing breakpoint mapping onto genes


gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.