chromo.regs-class: Class to store shattered regions and information produced by...

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

Description

Class to store shattered regions and information produced by shattered.regions and shattered.regions.cnv functions

Arguments

regions.summary	(list): a list of data.frames sumarizing the information of shattered regions found in each sample
high.density.regions	(matrix): a numeric matrix representing high breakpoint density genomic bins in each sample (values 1 = high density break; 0 = normal)
high.density.regions.hc	(matrix): a numeric matrix representing high breakpoint density genomic bins in each sample (values 1 = high density break; 0 = normal). Only those bins that overlap with high confidence regions defined in regions.summary are set to = 1
cnv.brk.dens	(matrix): a numeric matrix representing the number of CNV segmentation breakpoints found in at genomic bins in each sample
svc.brk.dens	(matrix): a numeric matrix representing the number of SV breakpoints found at genomic bins in each sample
cnv.brk.common.dens	(matrix): a numeric matrix representing the number of CNV breakpoints colocalizing SV breakpoints found at genomic bins in each sample
svc.brk.common.dens	(matrix): a numeric matrix representing the number of SV breakpoints colocalizing CNV breakpoints found at genomic bins in each sample
cnvbrk	(S4): on object generated by cnv.breaks function
svcbrk	(S4): on object generated by svc.breaks function
common.brk	(list): on object generated by match.breaks function
cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
svc	(S4) an object of class svcnvio containing data type 'svc' validated by validate.svc
param	(list): list of configuration parameters provided or set as default

Value

an instance of the class 'chromo.regs' containing breakpoint mapping onto genes

gonzolgarcia/svpluscnv documentation built on March 4, 2020, 10:06 a.m.