workflow_oncoscan.ascat: Run the standard workflow for ASCAT files (from oncoscan...
In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)
View source: R/workflow_oncoscan.R
workflow_oncoscan.ascat R Documentation
Run the standard workflow for ASCAT files (from oncoscan data).
Description
Run the standard workflow for ASCAT files (from oncoscan data).
Usage
workflow_oncoscan.ascat(ascat.fn)
Arguments
ascat.fn
Path to the text-export ASCAT file
Details
Identifies the globally altered arms (\>=90% of arm altered),
computes the HRD and TD+ scores. The amplification is defined as a CN>=5.
An arm is gained if of CN type cntype.gain unless the arm is
amplified.
Value
A list of lists with the following elements:
armlevel = list(AMP= list of arms, GAIN= list of arms, LOSS= list of
arms, LOH= list of arms),
scores = list(LST= number, LOH= number, TDplus= number, TD= number),
file = path of the ChAS file as given by the parameter)
Examples
segs.filename <- system.file('extdata', 'ascat_example.txt',
package = 'oncoscanR')
workflow_oncoscan.ascat(segs.filename)
yannchristinat/oncoscanR documentation built on Oct. 26, 2024, 12:58 p.m.
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.
View source: R/workflow_oncoscan.R
| workflow_oncoscan.ascat | R Documentation |
Run the standard workflow for ASCAT files (from oncoscan data).
Description
Run the standard workflow for ASCAT files (from oncoscan data).
Usage
workflow_oncoscan.ascat(ascat.fn)
Arguments
ascat.fn |
Path to the text-export ASCAT file |
Details
Identifies the globally altered arms (\>=90% of arm altered),
computes the HRD and TD+ scores. The amplification is defined as a CN>=5.
An arm is gained if of CN type cntype.gain unless the arm is
amplified.
Value
A list of lists with the following elements:
armlevel = list(AMP= list of arms, GAIN= list of arms, LOSS= list of
arms, LOH= list of arms),
scores = list(LST= number, LOH= number, TDplus= number, TD= number),
file = path of the ChAS file as given by the parameter)
Examples
segs.filename <- system.file('extdata', 'ascat_example.txt',
package = 'oncoscanR')
workflow_oncoscan.ascat(segs.filename)
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.