classifyProfile.rnaseq.svm: Expression profile classification

In sampleClassifier: Sample Classifier

Description

Function to classify RNA-seq gene expression profiles using support vector machines (SVM)

Usage

classifyProfile.rnaseq.svm(ref_matrix, query_mat, gene.ids.type="ensembl", fun1 = median)

Arguments

ref_matrix	RNA-seq data matrix to be used as reference, with genes corresponding to rows and samples corresponding to columns.
query_mat	RNA-seq query matrix to be classified, with genes corresponding to rows and samples corresponding to columns.
gene.ids.type	Type of the used gene identifiers, the following gene identifiers are supported: ensembl, refseq and ucsc gene ids. Default is ensembl.
fun1	mean or median. This will specify the number of marker genes that will be used for classification. Default is median.

Details

This function is based on the function svm from the R-package 'e1071'.

Value

A data frame with the predicted classes for each query profile.

Author(s)

Khadija El Amrani <[e-mail]>

Examples

library(sampleClassifierData)
data("se_rnaseq_refmat")
rnaseq_refmat <- assay(se_rnaseq_refmat)
data("se_rnaseq_testmat")
rnaseq_testmat <- assay(se_rnaseq_testmat)
res2.svm.df <- classifyProfile.rnaseq.svm(ref_matrix=rnaseq_refmat, query_mat=rnaseq_testmat, 
gene.ids.type="ensembl")
res2.svm.df

sampleClassifier documentation built on Jan. 21, 2021, 2:01 a.m.