fitcncf: Copy number and cellular fraction of segment clusters
In mskcc/facets: Cellular Fraction and Copy Numbers from Tumor Sequencing
Description
Usage
Arguments
Details
Value
Description
Fits the cluster specific copy number and cellular fraction based on
the cnlr.median and mafR values
Usage
1
fitcncf(out, dipLogR=0, nX=23)
Arguments
out
the out element from procSample fit
dipLogR
log-ratio level corresponding to diploid copy number
nX
integer value of ChrX; humans 23 (default); mouse 20.
Details
This function is called internally by procSample. It can be used to
refit the model at a different dipLogR value.
Value
A data frame with the same columns as out and three additional columns
which give the cellular fraction (cf), total copy number (tcn) and
lower copy number (lcn) for each segment. If a cluster does not have
sufficient heterozygotes the lcn value will be NA.
mskcc/facets documentation built on Oct. 15, 2021, 3:12 p.m.
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Description Usage Arguments Details Value
Description
Fits the cluster specific copy number and cellular fraction based on the cnlr.median and mafR values
Usage
1 | fitcncf(out, dipLogR=0, nX=23)
|
Arguments
out |
the out element from procSample fit |
dipLogR |
log-ratio level corresponding to diploid copy number |
nX |
integer value of ChrX; humans 23 (default); mouse 20. |
Details
This function is called internally by procSample. It can be used to refit the model at a different dipLogR value.
Value
A data frame with the same columns as out and three additional columns which give the cellular fraction (cf), total copy number (tcn) and lower copy number (lcn) for each segment. If a cluster does not have sufficient heterozygotes the lcn value will be NA.
R Package Documentation
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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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