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

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

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.