findMinIncCladeOfStrains: Finding out and summarising the minimal inclusive clade...
In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes
View source: R/func__findMinIncCladeOfStrains.R
findMinIncCladeOfStrains R Documentation
Finding out and summarising the minimal inclusive clade containing all given strains
Description
This function works in a similar way as the function findMinIncClade, except it works on a
given set of strains rather than a pair of alleles.
Usage
findMinIncCladeOfStrains(strains = NULL, clade.pam = NULL, clade.sizes = NULL)
Arguments
strains
a vector of strain names
clade.pam
a presence/absence matrix of samples in each clade of an input tree. It can be obtained
using the function tree2Clades of phylix.
clade.sizes
(optional) A named vector of integers for the number of samples in each clade. It can
be obtained from the element "sizes" in the outputs of the function tree2Clades. Optional.
Author(s)
Yu Wan (wanyuac@126.com)
Examples
mic <- findMinIncCladeOfStrains(strains = c("strain1", "strain2"), clade.pam = assoc[["struc"]][["clades"]][["pam"]],
clade.sizes = assoc[["struc"]][["clades"]][["sizes"]])
wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.
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View source: R/func__findMinIncCladeOfStrains.R
| findMinIncCladeOfStrains | R Documentation |
Finding out and summarising the minimal inclusive clade containing all given strains
Description
This function works in a similar way as the function findMinIncClade, except it works on a given set of strains rather than a pair of alleles.
Usage
findMinIncCladeOfStrains(strains = NULL, clade.pam = NULL, clade.sizes = NULL)
Arguments
strains |
a vector of strain names |
clade.pam |
a presence/absence matrix of samples in each clade of an input tree. It can be obtained using the function tree2Clades of phylix. |
clade.sizes |
(optional) A named vector of integers for the number of samples in each clade. It can be obtained from the element "sizes" in the outputs of the function tree2Clades. Optional. |
Author(s)
Yu Wan (wanyuac@126.com)
Examples
mic <- findMinIncCladeOfStrains(strains = c("strain1", "strain2"), clade.pam = assoc[["struc"]][["clades"]][["pam"]],
clade.sizes = assoc[["struc"]][["clades"]][["sizes"]])
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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