report_orthologs {orthogene}R Documentation

Report orthologs

Description

Identify the number of orthologous genes between two species.

Usage

report_orthologs(
  target_species = "mouse",
  reference_species = "human",
  standardise_genes = FALSE,
  method_all_genes = c("gprofiler", "homologene"),
  method_convert_orthologs = c("gprofiler", "homologene", "babelgene"),
  drop_nonorths = TRUE,
  non121_strategy = "drop_both_species",
  round_digits = 2,
  return_report = TRUE,
  verbose = TRUE,
  ...
)

Arguments

target_species

Target species.

reference_species

Reference species.

standardise_genes

If TRUE AND gene_output="columns", a new column "input_gene_standard" will be added to gene_df containing standardised HGNC symbols identified by gorth.

method_all_genes

R package to to use in all_genes step: "gprofiler" (slower but more species and genes) or "homologene" (faster but fewer species and genes).

method_convert_orthologs

R package to to use in convert_orthologs step: "gprofiler" (slower but more species and genes) or "homologene" (faster but fewer species and genes).

drop_nonorths

Drop genes that don't have an ortholog in the output_species.

non121_strategy

How to handle genes that don't have 1:1 mappings between input_species:output_species. Options include:

  • "drop_both_species" or "dbs" or 1 :
    Drop genes that have duplicate mappings in either the input_species or output_species
    (DEFAULT).

  • "drop_input_species" or "dis" or 2 :
    Only drop genes that have duplicate mappings in the input_species.

  • "drop_output_species" or "dos" or 3 :
    Only drop genes that have duplicate mappings in the output_species.

  • "keep_both_species" or "kbs" or 4 :
    Keep all genes regardless of whether they have duplicate mappings in either species.

  • "keep_popular" or "kp" or 5 :
    Return only the most "popular" interspecies ortholog mappings. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs.

  • "sum","mean","median","min" or "max" :
    When gene_df is a matrix and gene_output="rownames", these options will aggregate many-to-one gene mappings (input_species-to-output_species) after dropping any duplicate genes in the output_species.

round_digits

Number of digits to round to when printing percentages.

return_report

Return just the ortholog mapping between two species (FALSE) or return both the ortholog mapping as well a data.frame of the report statistics (TRUE).

verbose

Print messages.

...

Additional arguments to be passed to gorth or homologene.

NOTE: To return only the most "popular" interspecies ortholog mappings, supply mthreshold=1 here AND set method="gprofiler" above. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs.

For more details, please see here.

Value

List of ortholog report statistics

Examples

orth_fly <- report_orthologs(
    target_species = "fly",
    reference_species = "human"
)

[Package orthogene version 0.99.9 Index]