Extract summary table of clustering

Usage

extractTable(
  geneSetsList,
  resolution = NULL,
  summarize = TRUE,
  removeClusterId = TRUE
)

Arguments

geneSetsList: 'gsList' object with clusters and labels.
resolution: Numeric. Resolution to extract the table for. Default NULL uses the active resolution: the optimal resolution found by clusterGeneSets(), or the one last set with updateResolution() or updateClusterLabels().
summarize: Logical indicating whether to summarize the table by cluster (and source). Default is TRUE.
removeClusterId: Logical, if TRUE the cluster number will be removed from each cluster label. Default: TRUE.

Value

A data.frame. With summarize = TRUE, one row per cluster and source with the mean and standard deviation of the enrichment score (ignoring missing values) and the number of gene sets. With summarize = FALSE, one row per gene set and source with all columns of the 'enrichmentScore' slot plus its cluster; if a cluster label was changed with updateClusterLabels(), the original label is given in initial_cluster_label.

Examples

extractTable(exampleGsList)
#>       source               cluster enrichment mean enrichment sd genesets
#> 1 Expression             Stem Cell            1.27          0.07       81
#> 2   Splicing             Stem Cell            1.14            NA        1
#> 3 Expression        Serum Response            1.21          0.08       31
#> 4   Splicing        Serum Response            1.19          0.05       44
#> 5 Expression       Peptidyl Lysine            1.25            NA        1
#> 6   Splicing       Peptidyl Lysine            1.23          0.06       25
#> 7 Expression Carbonate Dehydratase            1.21          0.13       15
#> 8   Splicing Carbonate Dehydratase            1.23          0.17        8
head(extractTable(exampleGsList, resolution = 0.6, summarize = FALSE))
#>       source                                   pathway enrichment_score
#> 1 Expression GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP         1.294445
#> 2 Expression                     FISCHER_DREAM_TARGETS         1.223318
#> 3 Expression         MEBARKI_HCC_PROGENITOR_FZD8CRD_UP         1.282581
#> 4 Expression            VECCHI_GASTRIC_CANCER_EARLY_UP         1.283857
#> 5 Expression    SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP         1.420683
#> 6 Expression          KOBAYASHI_EGFR_SIGNALING_24HR_DN         1.340100
#>           pval         padj nlog10pval   cluster
#> 1 3.637638e-15 2.210229e-11  14.439181 Stem Cell
#> 2 3.314153e-14 1.006840e-10  13.479627 Stem Cell
#> 3 3.863003e-13 9.388643e-10  12.413075 Stem Cell
#> 4 2.789000e-11 4.236490e-08  10.554552 Stem Cell
#> 5 1.832008e-10 2.023870e-07   9.737073 Stem Cell
#> 6 3.091404e-10 2.889749e-07   9.509844 Stem Cell