fgsea_basic: Get results from fast Gene Set Enrichment Analysis (GSEA)
In mirvie/mirmisc: Non-Modeling Helper Functions For Mirvie R Coders

Description Usage Arguments Value See Also Examples

Uses fgsea::fgsea() defaults.

1	fgsea_basic(prepped_gsea_input_lfc, prepped_gsea_input_gene_set)

`prepped_gsea_input_lfc`	Output of `prep_gsea_input_lfc()`.
`prepped_gsea_input_gene_set`	Output of `prep_gsea_input_gene_set()`.

A dataframe.

Other Arkady: check_sample_descs(), collapse_tech_reps(), deseq_contrasts(), deseq_pairs(), deseq_wide(), plot_cond_paired_pearson(), plot_down(), plot_metrics_global(), plot_var_mean_ratio(), prep_gsea_input_gene_set(), prep_gsea_input_lfc(), prep_rd_input(), reconcile_names()

rs_genes <- arrow::read_feather(
  system.file("extdata", "rs_genes_draw_3_4.feather", package = "mirmisc")
)
rs_meta <- arrow::read_feather(
  system.file("extdata", "rs_meta_draw_3_4.feather", package = "mirmisc")
)
ddsx <- deseq_wide(rs_genes, rs_meta, compvar = "meta_draw")
dsq_contrasts <- deseq_contrasts(ddsx, compr = c("4", "3"))
prepped_gsea_input_lfc <- prep_gsea_input_lfc(dsq_contrasts)
prepped_gsea_input_gene_set <- prep_gsea_input_gene_set("C8")
fgsea_basic(prepped_gsea_input_lfc, prepped_gsea_input_gene_set)