QDNAseqCopyNumbers: Container for QDNAseq read count data

In QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

Description

Container for QDNAseq read count data

Assay data elements

An object of this class contains the following elements:

copynumber

(numeric) Corrected "count" signals in [0,+∞) An object with only this field is created by correctBins().

segmented

(numeric; optional) Segmented data in [0,+∞), added by calling segmentBins().

calls

(integer; optional) Calls as -2=deletion, -1=loss, 0=normal, 1=gain, 2=amplification, added by calling callBins().

probdloss

(numeric; optional) Probabilities of deletions in [0,1], added by calling callBins().

probloss

(numeric; optional) Probabilities of losses in [0,1], added by calling callBins().

probnorm

(numeric; optional) Probabilities of normal copy number in [0,1], added by calling callBins().

probgain

(numeric; optional) Probabilities of gains in [0,1], added by calling callBins().

probamp

(numeric; optional) Probabilities of amplifications in [0,1], added by calling callBins().

Missing values

The bin data (assay data) may contain missing values.

Author(s)

Ilari Scheinin

QDNAseq documentation built on Nov. 8, 2020, 6:57 p.m.