classifyProfile.rnaseq: Expression profile classification

In sampleClassifier: Sample Classifier

Description

Function to classify RNA-seq gene expression profiles

Usage

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

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.
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.

Details

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.

Value

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

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

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