predict_bccs_frequency: Frequency of BCCS subtype prediction
In sbuechler/BCCSclassifier: Breast Cancer Consensus Subtype Classifier
Description
Usage
Arguments
Value
Description
A function to predict for each sample and subtype, the fraction of
kTSP models in the family that predict the sample is in the subtype.
Learn more in vignette("BCCSclassifier")
Usage
1
predict_bccs_frequency(dat, model)
Arguments
dat
An object of class matrix with samples as column names and gene symbols
as row names, and entries the corresponding expression levels. The included tibble
bccs_classifier_genes contains the gene symbols and ENTREZIDs used in the
BCCSclassifier models, along with Affymetrix (hgu133a) and Illumina
(illuminaHuman v3) probes that can be used to represent the associated genes.
Expression values must not be scaled or median-centered.
model
A character string that is one of "erposneg", "erpos", "erneg",
to determine whether BCCSclassifier(ER+/-), BCCSclassifier(ER+), or
BCCSclassifier(ER-) should be used for subtyping.
Value
The output is a tibble (data.frame) with columns sample, subtype_prediction,
frequency. There is one record for each sample in the column names of dat and
each possible subtype. frequency is the fraction of kTSP models in
the family that predicted the sample was in the corresponding subtype.
sbuechler/BCCSclassifier documentation built on Dec. 22, 2021, 10:19 p.m.
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Description Usage Arguments Value
Description
A function to predict for each sample and subtype, the fraction of kTSP models in the family that predict the sample is in the subtype.
Learn more in vignette("BCCSclassifier")
Usage
1 | predict_bccs_frequency(dat, model)
|
Arguments
dat |
An object of class matrix with samples as column names and gene symbols
as row names, and entries the corresponding expression levels. The included tibble
|
model |
A character string that is one of "erposneg", "erpos", "erneg", to determine whether BCCSclassifier(ER+/-), BCCSclassifier(ER+), or BCCSclassifier(ER-) should be used for subtyping. |
Value
The output is a tibble (data.frame) with columns sample, subtype_prediction,
frequency. There is one record for each sample in the column names of dat and
each possible subtype. frequency is the fraction of kTSP models in
the family that predicted the sample was in the corresponding subtype.
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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