Correlation: Co-occurrence calculation
In schuyler-smith/phylosmith: Functions to help analyze data as phyloseq objects
Correlation R Documentation
Co-occurrence calculation
Description
Calculate the pair-wise Spearman rank correlation.
Usage
Correlation(X, Y,
cor_coef_cutoff, p_cutoff, method, ncores)
Arguments
X
An otu_table in the format from
phyloseq
Y
An otu_table in the format from
phyloseq
cor_coef_cutoff
double representing the minimum rho-value
accepted for the correlation to be returned.
p_cutoff
double representing the maximum p-value
accepted for the correlation to be returned.
method
Pearson, Spearman
ncores
An int for how many cores to use to multithread the
calculations.
Value
A data.frame with treatment, otu_1, otu_2, rho, p values.
Author(s)
Schuyler D. Smith
See Also
co_occurrence
schuyler-smith/phylosmith documentation built on Aug. 17, 2024, 10:19 a.m.
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| Correlation | R Documentation |
Co-occurrence calculation
Description
Calculate the pair-wise Spearman rank correlation.
Usage
Correlation(X, Y,
cor_coef_cutoff, p_cutoff, method, ncores)
Arguments
X |
An |
Y |
An |
cor_coef_cutoff |
|
p_cutoff |
|
method |
Pearson, Spearman |
ncores |
An |
Value
A data.frame with treatment, otu_1, otu_2, rho, p values.
Author(s)
Schuyler D. Smith
See Also
co_occurrence
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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