getMarkerGenes.rnaseq.html {MGFR} | R Documentation |
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)
getMarkerGenes.rnaseq.html(data.mat, samples2compare="all", gene.ids.type="ensembl",score.cutoff=1, directory = getwd())
data.mat |
RNA-seq gene expression matrix with genes corresponding to rows and samples corresponding to columns. |
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. |
This function is based on the function htmlpage from the R-package 'annotate'.
This function is used only for the side effect of creating HTML tables.
Khadija El Amrani <khadija.el-amrani@charite.de>
data(ref.mat) getMarkerGenes.rnaseq.html(ref.mat, samples2compare="all", gene.ids.type="ensembl", score.cutoff=1,directory = getwd())