getMarkerGenes.rnaseq.html {MGFR} | R Documentation

## Marker Gene Detection

### Description

Function to detect marker genes using normalized RNA-seq data and show the marker genes in HTML tables with links to various online annotation sources (Ensembl, GenBank and EntrezGene repositories)

### Usage

    getMarkerGenes.rnaseq.html(data.mat, class.vec=colnames(data.mat), samples2compare="all", gene.ids.type="ensembl",score.cutoff=1, directory = getwd())

### Arguments

`data.mat` | RNA-seq gene expression matrix with genes corresponding to rows and samples corresponding to columns.
`class.vec` | A character vector containing the classes of samples (columns) of data.mat in the same order as provided in the matrix.
`samples2compare` | A character vector with the sample names to be compared (e.g. c("liver", "lung", "brain")). By default all samples in the reference matrix are used.
`gene.ids.type` | Type of the used gene identifiers, the following gene identifiers are supported: ensembl, refseq and ucsc gene ids. default is ensembl.
`score.cutoff` | A value in the interval [0,1] to filter the markers according to the specificity score. The default value is 1 (no filtering).
`directory` | Path to the directory where to save the html pages, default is the current working directory.

### Details

This function is based on the function htmlpage from the R-package 'annotate'.

### Value

This function is used only for the side effect of creating HTML tables.

### Author(s)

Khadija El Amrani <a.khadija@gmx.de>

### Examples

    data(ref.mat)
    getMarkerGenes.rnaseq.html(ref.mat, class.vec = colnames(ref.mat), samples2compare="all", gene.ids.type="ensembl", score.cutoff=1,directory = getwd())

[Package MGFR version 1.10.1 Index]