calc_clonal_diversity: function to calculate shannon or simpson diversity of clonal...
In amf71/cloneMap: A Package to Construct Visual Representations of the Spatial Distribution of Somatic Clones in a Tissue / Sample
calc_clonal_diversity R Documentation
function to calculate shannon or simpson diversity of clonal
prevalence from CCF table input
Description
clonal prevalence indicates, for each clone,
what percentage of cells actually contain its
precise genotype (i.e. do not also have any other
additional mutations in subclones). Prevalence
for all clones should sum 100
Usage
calc_clonal_diversity(CCF.data, tree, method = "shannon")
Arguments
CCF.data
a table of clone CCFs with column 1 (named 'clone') specifying clone names and
column 2 (name 'CCF') specifying CCFs as either fractions or percentages
tree
a phylogenetic tree matrix with two column specifying 'parent' (column 1) and child (column 2)
method
which method of diversity calculation should be used. These are borrows from the 'diversity'
function of the 'vegan' package and can be "shannon", "simpson" or "invsimpson"
amf71/cloneMap documentation built on Jan. 11, 2024, 5:28 a.m.
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| calc_clonal_diversity | R Documentation |
function to calculate shannon or simpson diversity of clonal prevalence from CCF table input
Description
clonal prevalence indicates, for each clone, what percentage of cells actually contain its precise genotype (i.e. do not also have any other additional mutations in subclones). Prevalence for all clones should sum 100
Usage
calc_clonal_diversity(CCF.data, tree, method = "shannon")
Arguments
CCF.data |
a table of clone CCFs with column 1 (named 'clone') specifying clone names and column 2 (name 'CCF') specifying CCFs as either fractions or percentages |
tree |
a phylogenetic tree matrix with two column specifying 'parent' (column 1) and child (column 2) |
method |
which method of diversity calculation should be used. These are borrows from the 'diversity' function of the 'vegan' package and can be "shannon", "simpson" or "invsimpson" |
R Package Documentation
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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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