readFubarTable: Parses a FUBAR output table for significant posterior...
In asishallab/GeneFamilies: Analyses different properties of gene families
View source: R/selection_funks.R
readFubarTable R Documentation
Parses a FUBAR output table for significant posterior probabilities of a
codon being subject to positive selection. If any codons fit the criteria, a
respective table is returned, otherwise NULL is returned.
Description
Parses a FUBAR output table for significant posterior probabilities of a
codon being subject to positive selection. If any codons fit the criteria, a
respective table is returned, otherwise NULL is returned.
Usage
readFubarTable(path.2.fubar.csv, family.name, sign.post.prob = 0.9)
Arguments
path.2.fubar.csv
a valid file path to the FUBAR csv file to parse
family.name
A string indicating the name of the gene cluster (family)
subjected to the FUBAR analysis.
sign.post.prob
The cutoff value the posterior probabilities have to
meet (>=) in order to be considered significant. Default is
.9.
Value
An instance of base::data.frame holding the tabular FUBAR output
with just the following columns: 1. Codon, 2. Post.Prob, 3. BayesFactor, and
4. family. NULL is returned if no codon matches the significance
criteria.
asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.
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View source: R/selection_funks.R
| readFubarTable | R Documentation |
Parses a FUBAR output table for significant posterior probabilities of a
codon being subject to positive selection. If any codons fit the criteria, a
respective table is returned, otherwise NULL is returned.
Description
Parses a FUBAR output table for significant posterior probabilities of a
codon being subject to positive selection. If any codons fit the criteria, a
respective table is returned, otherwise NULL is returned.
Usage
readFubarTable(path.2.fubar.csv, family.name, sign.post.prob = 0.9)
Arguments
path.2.fubar.csv |
a valid file path to the FUBAR csv file to parse |
family.name |
A string indicating the name of the gene cluster (family) subjected to the FUBAR analysis. |
sign.post.prob |
The cutoff value the posterior probabilities have to
meet ( |
Value
An instance of base::data.frame holding the tabular FUBAR output
with just the following columns: 1. Codon, 2. Post.Prob, 3. BayesFactor, and
4. family. NULL is returned if no codon matches the significance
criteria.
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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