prepare_genesize_control_network: Prepare genesize control network

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Prepare genesize control network

Description

prepare_genesize_control_network takes a gene list and finds semi-randomly selected gene lists which are matched for gene length and GC content.

Usage

prepare_genesize_control_network(
  hits,
  bg = NULL,
  reps = 10000,
  no_cores = 1,
  sctSpecies = NULL,
  genelistSpecies = NULL,
  verbose = TRUE,
  localHub = FALSE
)

Arguments

hits	List of gene symbols containing the target gene list. Will automatically be converted to human gene symbols if geneSizeControl=TRUE.
bg	List of gene symbols containing the background gene list (including hit genes). If bg=NULL, an appropriate gene background will be created automatically.
reps	Number of gene lists to sample.
no_cores	Number of cores to parallelise bootstrapping reps over.
sctSpecies	Species that sct_data is currently formatted as (no longer limited to just "mouse" and "human"). See list_species for all available species.
genelistSpecies	Species that hits genes came from (no longer limited to just "mouse" and "human"). See list_species for all available species.
verbose	Print messages.
localHub	If working offline, add argument localHub=TRUE to work with a local, non-updated hub; It will only have resources available that have previously been downloaded. If offline, Please also see BiocManager vignette section on offline use to ensure proper functionality.

Value

A list containing three data frames:

• hits: Array of HGNC symbols containing the hit genes. May be slightly reduced if gene length / GC content could not be found for all genes.

• list_network: The control gene lists as a data frame of HGNC symbols

NathanSkene/EWCE documentation built on Nov. 3, 2024, 8:16 a.m.