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 1.0.0
Index]