CNAclinicData: An S4 class to contain the copy number, segmentation and...
In sdchandra/CNAclinic: A Software Suite for Shallow Sequencing Copy Number Analysis
chromosomes,CNAclinicData-method R Documentation
An S4 class to contain the copy number, segmentation and calls from
multiple samples.
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
## S4 method for signature 'CNAclinicData'
chromosomes(object)
sdchandra/CNAclinic documentation built on Aug. 8, 2024, 4:08 p.m.
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| chromosomes,CNAclinicData-method | R Documentation |
An S4 class to contain the copy number, segmentation and calls from multiple samples.
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
## S4 method for signature 'CNAclinicData'
chromosomes(object)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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