| Title: | Marker Gene Finder in RNA-seq data |
|---|---|
| Description: | The package is designed to detect marker genes from RNA-seq data. |
| Authors: | Khadija El Amrani |
| Maintainer: | Khadija El Amrani <[email protected]> |
| License: | GPL-3 |
| Version: | 1.31.0 |
| Built: | 2024-07-15 05:20:08 UTC |
| Source: | https://github.com/bioc/MGFR |
The package is designed to detect marker genes from RNA-seq data
| Package: | MGFR |
| Type: | Package |
| Version: | 1.9.2 |
| License: | GPL-3 |
Khadija El Amrani Maintainer: Khadija El Amrani <[email protected]>
data(ref.mat) res.list <- getMarkerGenes.rnaseq(ref.mat, class.vec=colnames(ref.mat), samples2compare="all", annotate=TRUE, gene.ids.type="ensembl", score.cutoff=1) names(res.list) ## show the first 20 markers of liver res.list[["liver_markers"]][1:20]data(ref.mat) res.list <- getMarkerGenes.rnaseq(ref.mat, class.vec=colnames(ref.mat), samples2compare="all", annotate=TRUE, gene.ids.type="ensembl", score.cutoff=1) names(res.list) ## show the first 20 markers of liver res.list[["liver_markers"]][1:20]
Function to detect marker genes using normalized RNA-seq data
getMarkerGenes.rnaseq(data.mat, class.vec=colnames(data.mat), samples2compare="all", annotate=FALSE, gene.ids.type="ensembl", score.cutoff=1)getMarkerGenes.rnaseq(data.mat, class.vec=colnames(data.mat), samples2compare="all", annotate=FALSE, gene.ids.type="ensembl", score.cutoff=1)
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. |
annotate |
A boolean value. If TRUE the gene symbol and the entrez gene id are shown. |
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). |
For each marker in the output list, the gene id and the corresponding score are shown. If annotate is TRUE, the gene symbol and the entrez gene id are shown. The score is used to rank the markers according to their specificity. A lower value means a higher specificity.
A list with marker genes associated with each sample type.
Khadija El Amrani <[email protected]>
data(ref.mat) res.list <- getMarkerGenes.rnaseq(ref.mat, class.vec = colnames(ref.mat), samples2compare="all", annotate=TRUE, gene.ids.type="ensembl", score.cutoff=1) names(res.list) ## show the first 20 markers of liver res.list[["liver_markers"]][1:20]data(ref.mat) res.list <- getMarkerGenes.rnaseq(ref.mat, class.vec = colnames(ref.mat), samples2compare="all", annotate=TRUE, gene.ids.type="ensembl", score.cutoff=1) names(res.list) ## show the first 20 markers of liver res.list[["liver_markers"]][1:20]
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, class.vec=colnames(data.mat), samples2compare="all", gene.ids.type="ensembl",score.cutoff=1, directory = getwd())getMarkerGenes.rnaseq.html(data.mat, class.vec=colnames(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. |
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. |
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 <[email protected]>
data(ref.mat) getMarkerGenes.rnaseq.html(ref.mat, class.vec = colnames(ref.mat), samples2compare="all", gene.ids.type="ensembl", score.cutoff=1,directory = getwd())data(ref.mat) getMarkerGenes.rnaseq.html(ref.mat, class.vec = colnames(ref.mat), samples2compare="all", gene.ids.type="ensembl", score.cutoff=1,directory = getwd())
RNA-seq gene expression data set derived from 5 tissue types (lung, liver, heart, kidney, and brain) from the ArrayExpress database (E-MTAB-1733). Each tissue type is represented by 3 replicates.
data(ref.mat)data(ref.mat)
A matrix with 32431 genes and 15 samples.
RNA-seq data matrix
data(ref.mat)data(ref.mat)