runPAM: Run partition around medoids classifier

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

Using partition around medoids (PAM) classifier to predict potential subtype label on external cohort and calculate in-group proportions (IGP) statistics.

Usage

runPAM(
  train.expr = NULL,
  moic.res = NULL,
  test.expr = NULL,
  gene.subset = NULL
)

Arguments

train.expr	A matrix of normalized expression training data with rows for genes and columns for samples; FPKM or TPM without log2 transformation is recommended.
moic.res	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
test.expr	A matrix of normalized expression testing data with rows for genes and columns for samples; FPKM or TPM without log2 transformation is recommended.
gene.subset	A string vector to indicate a subset of genes to be used.

Details

This function first trains a partition around medoids (PAM) classifier in the discovery (training) cohort to predict the subtype for patients in the external validation (testing) cohort, and each sample in the validation cohort was assigned to a subtype label whose centroid had the highest Pearson correlation with the sample. Finally, the in-group proportion (IGP) statistic will be performed to evaluate the similarity and reproducibility of the acquired subtypes between discovery and validation cohorts.

Value

A list with the following components:

IGP a named numeric vector storing the in-group proportion (see IGP.clusterRepro).

clust.res similar to 'clust.res' returned by 'getMOIC()' or 'get

mo.method a string value indicating the method used for prediction.

References

Tibshirani R, Hastie T, Narasimhan B and Chu G (2002). Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci, 99,6567–6572.

Kapp A V, Tibshirani R. (2007). Are clusters found in one dataset present in another dataset?. Biostatistics, 8(1):9-31.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.