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Perform Gene Set Enrichment Analysis (GSEA) on plant single-cell data.

Source: R/RunGSEA_plant.R
RunGSEA_plant.Rd

Perform Gene Set Enrichment Analysis (GSEA) on Seurat object. GSEA is implemented using clusterProfiler package. This function is only for three plant species: Arabidopsis thaliana or Oryza sativa or Zea mays.

Usage

RunGSEA_plant(
  SeuratObj,
  by = "GO",
  TERM2GENE = NULL,
  GeneIDtype = "TAIR",
  minpct = 0,
  release_version = "TAIR10"
)

Arguments

SeuratObj

Seurat object

by

GO, KEGG. Will be ignored if parameter "TERM2GENE" is not NULL.

TERM2GENE

Customized terms. Annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene. NULL by default. If not NULL, parameter "by" will be ignored.

GeneIDtype

Gene ID type in Seurat object. TAIR for Arabidopsis thaliana, for example. This parameter only works when SeuratObj@misc$species == 'Arabidopsis thaliana'.

minpct

Minimum expressed percent in each cluster, used to filter differentially expressed genes to run GSEA. 0 as default.

release_version

Release version of genome annotation. 'IRGSP-1.0' or 'v7.0' for Oryza sativa. 'Zm-B73-REFERENCE-NAM-5.0' or 'RefGen_V4' for Zea mays. This parameter will be ignored if SeuratObj@misc$species == 'Arabidopsis thaliana'.

Value

Seurat object

Examples

if (FALSE) {
SeuratObj <- RunGSEA_plant(SeuratObj, by = 'GO')
}