callEnsemble: callEnsemble

In huangwb8/GSClassifier: Gene Signature Classifier

callEnsemble

Description

Make subtype calls for each sample

Usage

callEnsemble(
  X,
  ens = NULL,
  geneAnnotation = NULL,
  geneSet = NULL,
  scaller = NULL,
  geneid = "ensembl",
  matchmode = c("fix", "free")[1],
  subtype = c("PAD.train_20200110", "ImmuneSubtype")[1],
  verbose = T
)

Arguments

X	a numeric RNA expression vector or matrix with gene names
ens	A List of multiple model. Result of fitEnsembleModel
geneAnnotation	A data frame with ENSEMBL, SYMBOL and ENTREZID of the genes in geneSet
geneSet	A list of genes for classification
scaller	scaller object. A xgb.train object.
geneid	type of gene id in X. One of 'symbol', 'entrez' and 'ensembl'.
matchmode	If your genes belong to ENSEMBL, SYMBOL or ENTREZ, you should set matchmode = 'fix', in which all genes would be aligned to ENSEMBL. 'matchmode = free' is a legacy feature, which means that you have to convert your genes into the same annotation type of the pre-trained GSClassifier model.
subtype	Default subtype methods. Now, only 'PAD' and 'ImmuneSubtype' are available. ATTENTION: If you use self-defined data (ens, geneAnnoation, geneSet or scaller), you MUST set subtype as NULL! All available options please visit GSClassifier_Data
verbose	whether report messages

Value

table, column 1 is best call, remaining columns are subtype prediction scores.

Examples

## X is a matrix with SYMBOL ID in row scale.
resIS <- callEnsemble(
X,
ens = NULL,
geneAnnotation = NULL,
geneSet = NULL,
geneid = "symbol",
nClust = 6,
subtype = 'ImmuneSubtype',
bestMethod = c("maximum", "scaller")[2],
scaller = NULL
)

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