retrieveGenesInfo-scRNAseq: retrieveGenesInfo

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

retrieveGenesInfo

Description

This method retrieve information about the marker genes of each cluster querying the Ensembl database with biomaRt and display the result.

Usage

retrieveGenesInfo(theObject, groupBy="clusters",
                orderGenes="initial", getUniprot=TRUE, cores=2,
                saveInfos=FALSE)

Arguments

theObject	An Object of class scRNASeq for which the count matrix was normalized (see ?normaliseCountMatrix), tSNE were calculated (see ?generateTSNECoordinates), dbScan was run (see ?runDBSCAN), cells were clustered (see ?clusterCellsInternal), as clusters themselves (see ?calculateClustersSimilarity), and ?rankGenes as ?retrieveTopMarkers.
groupBy	A column in the input table used for grouping the genes in the output tables. This option is useful if a table contains genes from different clusters. Default = "clusters".
orderGenes	If "initial" then the order of genes will not be changed. The other option is "alphabetical". Default = "initial".
getUniprot	Boolean, whether to get information from UniProt or not. Default = TRUE.
cores	Maximum number of jobs that CONCLUS can run in parallel. Default is 1.
saveInfos	If TRUE, save the genes infos table in the directory defined in theObject (?getOutputDirectory), in the sub-directory 'marker_genes/saveGenesInfo'.

Details

The output dataframe is composed of the following columns:

- uniprot_gn_symbol: Uniprot gene symbol.
- clusters: The cluster to which the gene is associated.
- external_gene_name: The complete gene name.
- go_id: Gene Ontology (GO) identification number.
- mgi_description: If the species is mouse, description of the gene on MGI.
- entrezgene_description: Description of the gene by Entrez database.
- gene_biotype: protein coding gene, lincRNA gene, miRNA gene, unclassified non-coding RNA gene, or pseudogene.
- chromosome_name: The chromosome on which the gene is located.
- Symbol: Official gene symbol.
- ensembl_gene_id: ID of the gene on the ensembl database.
- mgi_id: If the species is mouse, ID of the gene on the MGI database.
- entrezgene_id: ID of the gene on the entrez database.
- uniprot_gn_id: ID of the gene on the uniprot database.

Value

Display a table with the info retrieved.

Author(s)

Ilyess RACHEDI, based on code by Polina PAVLOVICH and Nicolas DESCOSTES.

See Also

rankGenes retrieveTopClustersMarkers

Examples

## Object scr containing the results of previous steps
load(system.file("extdata/scrFull.Rdat", package="conclus"))

## Getting genes info
scr <- retrieveGenesInfo(scr, cores=2)

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.