classifyProfile.rnaseq.svm {sampleClassifier} | R Documentation |
Function to classify RNA-seq gene expression profiles using support vector machines (SVM)
classifyProfile.rnaseq.svm(ref_matrix, query_mat, gene.ids.type="ensembl", fun1 = median)
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. |
This function is based on the function svm from the R-package 'e1071'.
A data frame with the predicted classes for each query profile.
Khadija El Amrani <khadija.el-amrani@charite.de>
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