subfunctionalizationAnnotationBased: Identifies instances of subfunctionalization occurred in the...
In asishallab/GeneFamilies: Analyses different properties of gene families
View source: R/annotationVectorSpace.R
subfunctionalizationAnnotationBased R Documentation
Identifies instances of subfunctionalization occurred in the evolution from
the base genes to the evolved genes. Subfunc. is identified based on the
gene annotations. All possible combinations of evolved genes are tested with
each base gene. Subfunc conditions are 1. The tested evolved genes
annotations (EA) are not a superset of the base gene annotations (BGA), 2.
the intersection of EA is smaller than the union of EA, and 3. The union of
EA is identical to the BGA, or, if not strict, the union of the EA is a
subset of the BGA.
Description
Identifies instances of subfunctionalization occurred in the evolution from
the base genes to the evolved genes. Subfunc. is identified based on the
gene annotations. All possible combinations of evolved genes are tested with
each base gene. Subfunc conditions are 1. The tested evolved genes
annotations (EA) are not a superset of the base gene annotations (BGA), 2.
the intersection of EA is smaller than the union of EA, and 3. The union of
EA is identical to the BGA, or, if not strict, the union of the EA is a
subset of the BGA.
Usage
subfunctionalizationAnnotationBased(base.genes, evolved.genes,
annot.df = all.ipr, gene.col = 1, annot.col = 2, strict = TRUE)
Arguments
base.genes
Character vector of gene IDs, identifying the base genes.
evolved.genes
Character vector of gene IDs, identifying the evolved
genes.
annot.df
A data.frame of gene annotations. Default is
GeneFamilies::all.ipr
gene.col
The column name or index in annot.df in which to
lookup the gene IDs. Default is 1
strict
Boolean indicating whether to apply the strict criterium in
the second condition, or not (see above for details). Default is
TRUE.
anno.col
The column name or index in annot.df in which to
lookup the gene annotations. Default is 2.
Value
NA if there are no annotations for at least one base gene and
at least two evolved.genes. NULL is returned if the previous
conditions are met, but no subfunctionilizations could be identified, and
finally a data.frame is returned with the identified subfunctionilizations.
In this, columns are: base.gene, base.annotations, evolved.genes, and
evolved.annotations.
asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.
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View source: R/annotationVectorSpace.R
| subfunctionalizationAnnotationBased | R Documentation |
Identifies instances of subfunctionalization occurred in the evolution from the base genes to the evolved genes. Subfunc. is identified based on the gene annotations. All possible combinations of evolved genes are tested with each base gene. Subfunc conditions are 1. The tested evolved genes annotations (EA) are not a superset of the base gene annotations (BGA), 2. the intersection of EA is smaller than the union of EA, and 3. The union of EA is identical to the BGA, or, if not strict, the union of the EA is a subset of the BGA.
Description
Identifies instances of subfunctionalization occurred in the evolution from the base genes to the evolved genes. Subfunc. is identified based on the gene annotations. All possible combinations of evolved genes are tested with each base gene. Subfunc conditions are 1. The tested evolved genes annotations (EA) are not a superset of the base gene annotations (BGA), 2. the intersection of EA is smaller than the union of EA, and 3. The union of EA is identical to the BGA, or, if not strict, the union of the EA is a subset of the BGA.
Usage
subfunctionalizationAnnotationBased(base.genes, evolved.genes,
annot.df = all.ipr, gene.col = 1, annot.col = 2, strict = TRUE)
Arguments
base.genes |
Character vector of gene IDs, identifying the base genes. |
evolved.genes |
Character vector of gene IDs, identifying the evolved genes. |
annot.df |
A data.frame of gene annotations. Default is
|
gene.col |
The column name or index in |
strict |
Boolean indicating whether to apply the strict criterium in
the second condition, or not (see above for details). Default is
|
anno.col |
The column name or index in |
Value
NA if there are no annotations for at least one base gene and
at least two evolved.genes. NULL is returned if the previous
conditions are met, but no subfunctionilizations could be identified, and
finally a data.frame is returned with the identified subfunctionilizations.
In this, columns are: base.gene, base.annotations, evolved.genes, and
evolved.annotations.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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