score_td: Compute the number of large tandem duplication (TDplus).
In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)
score_td R Documentation
Compute the number of large tandem duplication (TDplus).
Description
Compute the number of large tandem duplication (TDplus).
Usage
score_td(segments)
Arguments
segments
A GRanges object containing the segments, their copy
number and copy number types.
Details
Procedure based on the paper from Popova et al., Cancer Res 2016
(PMID: 26787835). The TDplus score is defined as the number of regions larger
than 1Mb but smaller or equal to 10Mb with a gain of one or two copies. This
score was linked
to CDK12-deficient tumors. They also identified as second category of tandem
duplication whose size is smaller or equal than 1Mb and around 300Kb but
could not link it to a phenotype. Note that due to its resolution the
Oncoscan assay will most likely miss this second category. Nonetheless it
is reported by the function.
Value
A list of integer containing the TDplus score ('TDplus') and
the small TD score ('TD').
Examples
score_td(segs.chas_example)
yannchristinat/oncoscanR documentation built on Oct. 26, 2024, 12:58 p.m.
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| score_td | R Documentation |
Compute the number of large tandem duplication (TDplus).
Description
Compute the number of large tandem duplication (TDplus).
Usage
score_td(segments)
Arguments
segments |
A |
Details
Procedure based on the paper from Popova et al., Cancer Res 2016 (PMID: 26787835). The TDplus score is defined as the number of regions larger than 1Mb but smaller or equal to 10Mb with a gain of one or two copies. This score was linked to CDK12-deficient tumors. They also identified as second category of tandem duplication whose size is smaller or equal than 1Mb and around 300Kb but could not link it to a phenotype. Note that due to its resolution the Oncoscan assay will most likely miss this second category. Nonetheless it is reported by the function.
Value
A list of integer containing the TDplus score ('TDplus') and
the small TD score ('TD').
Examples
score_td(segs.chas_example)
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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