get_compared_gene_sets: Get compared gene sets
In YutongWangUMich/corgi: CORGI: Curve-fit Objective Ranking of Gene Importance.

Description Usage Arguments Value Examples

Gene sets compared against CorGI in the manuscript

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get_compared_gene_sets(batch1_top_genes, batch1_name = "Batch1",
  batch2_top_genes, batch2_name = "Batch2", desired_size,
  marker_genes = c())

`batch1_top_genes`	ordered list of genes (e.g., most highly variable to least)
`batch1_name`	name of batch1 (e.g., if `batch1_top_genes` was computed using highly variable genes (HVG), then consider `batch1_name <- HVG(Batch1)`)
`batch2_top_genes`	see `batch1_top_genes`
`batch2_name`	see `batch1_name`
`desired_size`	how big the output gene_sets should be
`marker_genes`	genes that are included in every gene set of the output. Defaults to the empty set, i.e., no markers provided.

a list of gene sets, where each item is a gene set of size desired_size. The list is ordered as follows:

batch1_top_genes[1:desired_size]
batch2_top_genes[1:desired_size]
union(batch1_top_genes[1:x], batch2_top_genes[1:y]) where x and y satisfies |x-y| <= 1
intersect(batch1_top_genes[1:x],batch2_top_genes[1:y]) where x and y satisfies |x-y| <= 1

If marker_genes is nonempty, then all four gene sets above include marker_genes.

HVG_batch1 <- c(paste0("g",1:4),paste0("g",7:10))
HVG_batch2 <- paste0("g",3:9)
marker_genes <- "g0"
get_compared_gene_sets(HVG_batch1, "HVG(batch1)", HVG_batch2, "HVG(batch2)", 6, marker_genes)