subtypeVector: subtypeVector

In huangwb8/GSClassifier: Gene Signature Classifier

subtypeVector

Description

Automatic clustering based on expression matrix and gene expression profiles

Usage

subtypeVector(
  expr,
  geneSet,
  cluster.method = c("ward.D2", "complete")[1],
  extra.annot = NULL,
  plot.title = NULL,
  k = NULL,
  outlier.filter = 2,
  verbose = T
)

Arguments

expr	RNA expression matrix. Samples in col and ENSEMBL genes in row.
geneSet	List. Gene expression profiles - Co-expressed modules from WGCNA, etc
cluster.method	One of 'ward.D2', 'complete' or other methods in hclust. If 'randomForest' was set, the randomForest function would used to classify the samples.
extra.annot	Extra top annotation. The same order as colnames of expr.
plot.title	The title of heatmap report.
k	the number of clusters you want. Default is the same as the number of geneSet types
outlier.filter	Integer. Set a small integer to remove outlier samples
verbose	Whether to show heatmap in the process.

Value

A list:

• Repeat Basic parameters

• Data mean expression of each GEP in each sample cluster

• logloss negative log-likelihood function

• MissGene Missing genes

• Plot a Heatmap object

Author(s)

Weibin Huang<[e-mail]>

huangwb8/GSClassifier documentation built on July 12, 2024, 5:10 p.m.