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 1.0.2 Index]