check_ewce_genelist_inputs

Source: R/check_ewce_genelist_input.r

check_ewce_genelist_inputs Is used to check that hits and bg gene lists passed to EWCE are setup correctly. Checks they are the appropriate length. Checks all hits are in bg. Checks the species match and if not reduces to 1:1 orthologs.

check_ewce_genelist_inputs(
  sct_data,
  hits,
  bg = NULL,
  genelistSpecies = NULL,
  sctSpecies = NULL,
  sctSpecies_origin = sctSpecies,
  output_species = "human",
  method = "homologene",
  geneSizeControl = FALSE,
  standardise_sct_data = TRUE,
  standardise_hits = FALSE,
  min_genes = 4,
  verbose = TRUE
)

Arguments

sct_data

List generated using generate_celltype_data.

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.

genelistSpecies

Species that hits genes came from (no longer limited to just "mouse" and "human"). See list_species for all available species.

sctSpecies

Species that sct_data is currently formatted as (no longer limited to just "mouse" and "human"). See list_species for all available species.

sctSpecies_origin

Species that the sct_data originally came from, regardless of its current gene format (e.g. it was previously converted from mouse to human gene orthologs). This is used for computing an appropriate backgrund.

output_species

Species to convert sct_data and hits to (Default: "human"). See list_species for all available species.

method

R package to use for gene mapping:

  • "gprofiler" : Slower but more species and genes.

  • "homologene" : Faster but fewer species and genes.

  • "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.

geneSizeControl

Whether you want to control for GC content and transcript length. Recommended if the gene list originates from genetic studies (Default: FALSE). If set to TRUE, then hits must be from humans.

standardise_sct_data

Should sct_data be standardised? if TRUE:

  • When sctSpecies!=output_species the sct_data will be checked for object formatting and the genes will be converted to the orthologs of the output_species with standardise_ctd (which calls map_genes internally).

  • When sctSpecies==output_species, the sct_data will be checked for object formatting with standardise_ctd, but the gene names will remain untouched.

standardise_hits

Should hits be standardised? If TRUE:

  • When genelistSpecies!=output_species, the genes will be converted to the orthologs of the output_species with convert_orthologs.

  • When genelistSpecies==output_species, the genes will be standardised with map_genes.

If FALSE, hits will be passed on to subsequent steps as-is.

min_genes

Minimum number of genes in a gene list to test.

verbose

Print messages.

Value

A list containing

  • hits: Array of MGI/HGNC gene symbols containing the target gene list.

  • bg: Array of MGI/HGNC gene symbols containing the background gene list.

Examples

ctd <- ewceData::ctd()
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache
example_genelist <- ewceData::example_genelist()
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache

# Called from "bootstrap_enrichment_test()" and "generate_bootstrap_plots()"
checkedLists <- EWCE::check_ewce_genelist_inputs(
    sct_data = ctd,
    hits = example_genelist,
    sctSpecies = "mouse",
    genelistSpecies = "human"
)
#> Checking gene list inputs.
#> Generating gene background for mouse x human ==> human
#> Gathering ortholog reports.
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Gene table with 19,129 rows retrieved.
#> Returning all 19,129 genes from human.
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: mouse
#> Common name mapping found for mouse
#> 1 organism identified from search: 10090
#> Gene table with 21,207 rows retrieved.
#> Returning all 21,207 genes from mouse.
#> --
#> --
#> Preparing gene_df.
#> data.frame format detected.
#> Extracting genes from Gene.Symbol.
#> 21,207 genes extracted.
#> Converting mouse ==> human orthologs using: homologene
#> Retrieving all organisms available in homologene.
#> Mapping species name: mouse
#> Common name mapping found for mouse
#> 1 organism identified from search: 10090
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Checking for genes without orthologs in human.
#> Extracting genes from input_gene.
#> 17,355 genes extracted.
#> Extracting genes from ortholog_gene.
#> 17,355 genes extracted.
#> Checking for genes without 1:1 orthologs.
#> Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
#> Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
#> Filtering gene_df with gene_map
#> Adding input_gene col to gene_df.
#> Adding ortholog_gene col to gene_df.
#> 
#> =========== REPORT SUMMARY ===========
#> Total genes dropped after convert_orthologs :
#>    4,725 / 21,207 (22%)
#> Total genes remaining after convert_orthologs :
#>    16,482 / 21,207 (78%)
#> --
#> 
#> =========== REPORT SUMMARY ===========
#> 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
#> 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
#> Gathering ortholog reports.
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Gene table with 19,129 rows retrieved.
#> Returning all 19,129 genes from human.
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Gene table with 19,129 rows retrieved.
#> Returning all 19,129 genes from human.
#> --
#> 
#> =========== REPORT SUMMARY ===========
#> 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
#> 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
#> 16,482 intersect background genes used.
#> Standardising sct_data.