Find similarities between expression profiles with fgsea. Mitochondrial/ribosomal genes are filtered from the analysis

Find similarities between expression profiles with fgsea. Mitochondrial/ribosomal genes are filtered from the analysis

Usage

compute_multi_screen_profile(
  data = NULL,
  target = NULL,
  geneset = NULL,
  n_genes_profile = 200,
  direction = "both",
  minSize = 15,
  maxSize = 500,
  num_cores = 1
)

Arguments

data

A tidyseurat object merged with metadata. Must contain columns "Well_ID", "Row", "Column".

target

Value of a target expression profile in data (target) against which the others should be compared to.

geneset

List of genes whose enrichment in expression profiles should be evaluated.

n_genes_profile

Number of genes to take for a target profile from a ranked list, default 200.

direction

Direction of the expression of DE genes in the target profile: one of "up", "down" and "both", default "both".

minSize

Minimum size of gene sets to consider (default 15).

maxSize

Maximum size of gene sets to consider (default 500).

num_cores

Number of cores to use for parallel processing.

Value

A tidyseurat object with screen_profile data frame in slot tools.

Examples

data(mini_mac)
mini_mac@tools$diff_exprs <- mini_mac@tools$diff_exprs[1:2]
mini_mac <- compute_multi_screen_profile(mini_mac, target = "Staurosporine_10",
n_genes_profile = 20, direction = "up", num_cores = 1)