Prepare genesize control network

Source: R/prepare_genesize_control_network.r

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

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