add_marker_genes_into_compendium: add_marker_genes_into_compendium

In VCCRI/C3: An R package for cross-species compendium-based cell-type identification for transcriptomic profile

Description

This function adds a set of marker genes to a marker gene compendium. The marker gene data can be a matrix with more than one cell type / tissue or a vector for a single cell type / tissue.

Usage

add_marker_genes_into_compendium(marker.gene.compendium, marker.genes,
  species = "hsapiens", data.format = "vector",
  geneID = "ensembl_gene_id")

Arguments

marker.gene.compendium	A list consisting of marker gene compendium, species, compendium common genes, as returned by make_marker_gene_compendium.
marker.genes	A list or vector containing marker genes. For a list, each element denotes cell type or tissue and contains a vector of marker gene names. For a vector, it is the names of the marker genes of a single cell or tissue. The name of this cell type or tissue will need to be manually updated.
species	The species abbreviation name of the marker genes.
data.format	The data format of the marker.genes, either 'vector' or 'list'. Default is "vector"
geneID	The code for the type of gene IDs used by sample.data, as used by the biomaRt database. To find the valid codes for gene IDs for a species, please see the find_valid_geneID() function of the C3 package. Default is "ensembl_gene_id".

Details

This function adds a set of marker genes to a marker gene compendium. The marker gene data can be a list with more than one cell type / tissue or a vector for a single cell type / tissue. This function adds only those marker genes that are exist in the marker gene compendium.

Value

This function returns a list by adding the new sample data into the marker gene compendium ('marker.genes.matrix').

Examples

## Here we will use "human.encode.data" and "human.encode.data.descriptor" from C3 repository to make the compendium.
## These data sets are loaded automatically with the package.
## The gene expression data sets are in list format. Here every list element contains transcriptomic profile data of a cell or tissue type.
human.compendium<-make_gene_expression_compendium(gene.expression.data=human.encode.data, experiment.descriptor=human.encode.data.descriptor, expression.data.format="list")

## Next we will make the marker gene compendium from the human.compendium
human.marker.gene.compendium<-make_marker_gene_compendium(compendium.data=human.compendium, specific.cutoff = 0.05, top.expressed.genes = 500)

## Finally we will add the marker genes of a cell type into the compendium
marker.genes<-c("CRYAA", "CRYAB", "CRYBB3", "PAX6", "SOX2", "PROX1", "CRYBA1", "BFSP2", "CRYBB2", "BIRC6")
human.marker.gene.compendium.update<-add_marker_genes_into_compendium(marker.gene.compendium = human.marker.gene.compendium, marker.genes = marker.genes, data.format = "vector", geneID = "external_gene_name")

## Here, we will see that all marker genes are added as a 'newly added' cell type in the marker gene compendium except 'PROX1' as it does not exist in the universe of the marker gene compendium
names(which(human.marker.gene.compendium.update$marker.genes.matrix[,1]==1))

VCCRI/C3 documentation built on May 14, 2019, 8:41 a.m.