CNAclinicData: An S4 class to contain the copy number, segmentation and...

Description Usage

Description

An object of this class contains several data.frame objects. bins contains information on binned genomic windows such as the chromosome, start and end of the bins as well as a condition to use or filter the bins. All other data.frames have rows corresponding to genomic bins and the columns to separate samples. Of these, copyNumber contains the bias corrected and normalized count data (log2 ratios), the others named segCBS, segHMM, segPLS and segLACBS contain the value of the segment for each genomic bin calculated from multiple segmentation algorithms. The segSummary data.frame holds the summarised consensus segment values for each bin and input sample, while calls holds the respective copy number calls.

Usage

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## S4 method for signature 'CNAclinicData'
chromosomes(object)

sdchandra/CNAclinic documentation built on May 29, 2019, 9:33 a.m.