getMarkerGenes: Get all markers for a specific cell type within a species

In klprint/markerDB: Give access to MarkerDB (http://markers.blebli.de)

Description

This functions gives a vector of annotated markers of a cell type within a predefined species.

Usage

getMarkerGenes(celltype, species, field = c("marker_accession",
  "marker_name"), positive = TRUE, filter_list = list(),
  exclusive = NULL, server = "http://markers.blebli.de")

Arguments

celltype	name of celltype
species	name of species (as can be found using getSpecies function)
field	can be either "marker_accession" to get GeneIDs or "marker_name" to return gene names
positive	True by default. Only return positive markers
filter_list	Additional filters in list format (i.e: list(stage = "p7")). Wildcards can be added by using a "%" sign. So, if all embryonic mouse markers are wanted, a list like list(stage="E%") can be used.
exclusive	Either Null, "all" or a vector with celltypes. If provided, only marker genes are returned that are exclusive to the celltype specified in "celltype" amongst all annotated markers or the celltypes given in this parameter.
server	URL of the server hosting the markerDB website.

Value

character vector of marker genes

klprint/markerDB documentation built on May 16, 2019, 4:09 a.m.