getMarkerGenes.rnaseq.html: Marker Gene Detection

In MGFR: Marker Gene Finder in RNA-seq data

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 <[e-mail]>

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())

MGFR documentation built on Nov. 8, 2020, 11:11 p.m.