subset_mem: Subset mem multienrichment object
In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

subset_mem

R Documentation

Subset mem multienrichment object

Description

Subset mem multienrichment object

Usage

subset_mem(
  mem,
  includeSets = NULL,
  includeGenes = NULL,
  min_gene_ct = 1,
  min_set_ct = 1,
  p_cutoff = NULL,
  verbose = FALSE,
  ...
)

Arguments

`mem`	`list` object as returned by `multiEnrichMap()`
`includeSets`	`character` vector with specific sets to retain, all other sets will be dropped.
`includeGenes`	`character` vector with specific genes to retain, all other genes will be dropped.
`min_gene_ct`	`numeric` filter applied to genes representing the minimum number of occurrences across sets in the `mem$memIM` incidence matrix. The default value `min_gene_ct=1` effectively requires a gene to be present in at least one set, which is useful after filtering by `includeSets`.
`min_set_ct`	`numeric` filter applied to sets representing the minimum number of occurrences of genes in the `mem$memIM` incidence matrix. The default value `min_set_ct=1` effectively requires a set to contain at least one gene.
`p_cutoff`	`numeric` optional enrichment P-value filter to apply to `mem$enrichIM` enrichment P-values. It is intended to apply optionally higher stringency by using a lower `p_cutoff` than used by `multiEnrichMap()`.
`verbose`	`logical` indicating whether to print verbose output.
`...`	additional arguments are ignored.

Details

This function is intended to subset the incidence matrix data contained in a mem object by heuristics. It does not update other data in the mem object such as enrichList and multiEnrichDF, nor any igraph objects. It is intended mainly to subset by sets (pathways), or genes, then also subset other corresponding incidence matrix data consistently.

Value

list object of mem data

Other jam utility functions: avg_angles(), avg_colors_by_list(), call_fn_ellipsis_deprecated(), cell_fun_bivariate(), collapse_mem_clusters(), colorRamp2D(), deconcat_df2(), display_colorRamp2D(), enrichList2geneHitList(), filter_mem_genes(), filter_mem_sets(), find_colname(), get_hull_data(), get_igraph_layout(), gsubs_remove(), handle_igraph_param_list(), isColorBlank(), make_legend_bivariate(), make_point_hull(), mem_find_overlap(), order_colors(), rank_mem_clusters(), rotate_coordinates(), subgraph_jam(), summarize_node_spacing(), xyAngle()