classifyProfile.rnaseq: Expression profile classification
In khadija-a/sampleClassifier: Sample Classifier

Description Usage Arguments Details Value Author(s) Examples

Function to classify RNA-seq gene expression profiles

1	classifyProfile.rnaseq(ref_matrix, query_mat, gene.ids.type="ensembl", fun1 = median, write2File=FALSE, out.dir=getwd())

`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.
`write2File`	A logical value. If TRUE the classification results will be written to a file.
`out.dir`	Path to the directory, in which to write the results. Default is the actual working directory.

Each query profile is compared to all sample types in the reference matrix and a similarity score is calculated. The similarity score is based on the number of marker genes that are shared between the query and the reference. These marker genes are given in a file if write2File is TRUE.

A list with top hits for each query profile, sorted according to a similarity score.

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.list <- classifyProfile.rnaseq(ref_matrix=rnaseq_refmat, query_mat=rnaseq_testmat, 
gene.ids.type="ensembl",write2File=FALSE)
res2.list