top_by_go: Select top_genes based on go terms

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Select top_genes based on go terms

Description

The clusterSet object contains a top_genes slot that can be used to display genes in heatmaps (see plot_heatmap function). Here the function select top_genes based on GO terms.

Usage

top_by_go(
  object,
  go_id = "GO:0003677",
  species = "hsapiens",
  gene_id = "hgnc_symbol",
  host = "https://www.ensembl.org"
)

Arguments

object	A ClusterSet object.
go_id	A GO ID.
species	The target species according to biomaRt::listDatasets(mart = ensembl)$dataset (e.g hsapiens, mmusculus, rnorvegicus...).
gene_id	The type of gene identifier in the clusterSet object (default hgnc_symbol). use biomaRt::listFilters() to get the vailable list.
host	Host to connect to. Defaults to www.ensembl.org.

Value

A ClusterSet object.

Examples

## Not run: 
# Set verbosity to 1 to display info messages only.
set_verbosity(1)

# Load a dataset
load_example_dataset('7871581/files/pbmc3k_medium_clusters')

# DNA Binding: "GO:0003677"
# Here only for cluster 1 and 2
pbmc3k_medium_clusters <- top_by_go(pbmc3k_medium_clusters[1:2, ], go_id = "GO:0003677")
pbmc3k_medium_clusters@top_genes

## End(Not run)

dputhier/scigenex documentation built on May 31, 2024, 8:59 a.m.