The gsList class — gsList-class • geneSetSimplifyR

A gsList holds the input and results of the geneSetSimplifyR workflow. It is created by initializeList(), filled by clusterGeneSets() and labelClusters(), or all at once by geneSetSimplifyR(). Use extractTable() to get the results as a table.

Usage

# S4 method for class 'gsList'
show(object)

Arguments

object: A 'gsList' object.

Value

gsList objects are created by initializeList(), not by calling the class generator directly. show() prints a summary of the object and returns it invisibly.

Functions

show(gsList): Print a short summary of the object.

Slots

genesetsDataframe: A data.frame with genes as rows and gene sets as columns; 1 if the gene is in the gene set, else 0.
enrichmentScore: A data.frame with one row per gene set and source: pathway, source, enrichment_score, pval, nlog10pval and any other column supplied to initializeList().
cluster: A Seurat object with the LSI, UMAP, SNN graph and the cluster of every gene set for each resolution (GSEA_snn_res.<resolution> metadata columns).
labels: A list with, for each resolution, the cluster labels (labelsDefault), the TF-IDF scores of the label candidates (labelsTFIDF) and the most central gene sets (labelsCentrality).
metadata: A list with parameters and results of the workflow, e.g. the number of nearest neighbors, the chosen resolution and silhouette scores.

Examples

exampleGsList
#> A gsList object with 197 gene sets from 2 source(s) clustered into 4 labeled clusters.
#> Metadata:
#>   algorithm: louvain
#>   k (KNN): 14
#>   LSI elbow cutoff: 11
#>   selected resolution: 0.1
#>   n pathways: 197
names(exampleGsList@metadata)
#>  [1] "n_genes"             "n_pathways"          "n_sources"          
#>  [4] "package_version"     "initialized_at"      "k"                  
#>  [7] "lsi_elbow_cutoff"    "cluster_algorithm"   "resolutions_tested" 
#> [10] "selected_resolution" "active_resolution"   "silhouette_scores"  
#> [13] "clustered_at"        "n_labels"            "remove_first_word"  
#> [16] "stop_words"          "labeled_at"