make.heldout.obj: tcsm's internal function to calculate likelihood for each 'K'...
In WuyangFF95/SynSigRun: Run Mutational Signature Analysis Software Packages Using Mutational Spectra generated by SynSigGen
make.heldout.obj R Documentation
tcsm's internal function to calculate likelihood for each K
using heldout method.
Description
This code requires the CRAN package stm https://cran.r-project.org/package=stm.
Usage
make.heldout.obj(train.mc.data, test.mc.data)
Arguments
train.mc.data
Transposed ICAMS spectra catalog
containing mutations of training samples.
test.mc.data
Transposed ICAMS spectra catalog
containing mutations of testing samples.
Details
tcsm advises to use "heldout" method to obtain the likelihood of number of
mutational signatures, K.
That is, to split the whole spectra catalogs dataset into 2 parts:
80
for training stm model,
20
for estimating likelihood for given K.
Value
heldout, which is a named list
$missing
$index
$docs - list where each element is a list containing the mutations for a given sample
$documents - list where each element is a list containing the mutations for a given sample
$vocab - list the vocabularies, which refers to mutation types.
WuyangFF95/SynSigRun documentation built on Oct. 7, 2022, 1:16 p.m.
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| make.heldout.obj | R Documentation |
tcsm's internal function to calculate likelihood for each K
using heldout method.
Description
This code requires the CRAN package stm https://cran.r-project.org/package=stm.
Usage
make.heldout.obj(train.mc.data, test.mc.data)
Arguments
train.mc.data |
Transposed |
test.mc.data |
Transposed |
Details
tcsm advises to use "heldout" method to obtain the likelihood of number of
mutational signatures, K.
That is, to split the whole spectra catalogs dataset into 2 parts:
80
for training stm model,
20
for estimating likelihood for given K.
Value
heldout, which is a named list $missing $index $docs - list where each element is a list containing the mutations for a given sample $documents - list where each element is a list containing the mutations for a given sample $vocab - list the vocabularies, which refers to mutation types.
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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