FeatureCorrelation: Main function to calculate correlation of all other feature...
In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.
FeatureCorrelation R Documentation
Main function to calculate correlation of all other feature to a given feature name
Description
This functions calculate correlation of all other feature to a given feature name.
This is used in the Pattern Search analysis.
Usage
FeatureCorrelation(mbSetObj, dist.name, taxrank, feat)
Arguments
mbSetObj
Input the name of the mbSetObj.
dist.name
Input the distance measure. Input "pearson" for
Pearson R, "spearman" for Spearman rank correlation, and "kendall"
for Kendall rank correlation.
taxrank
Character, input the taxonomic level to use.
taxa
If the pattern is defined by using a specific taxon, input the name
of that taxa here.
variable
Input the name of the experimental factor.
datatype
If the data is marker gene, input "16S". If the
data is metagenomic, use "metageno".
shotfeat
Only valid for SDP module, set to "null".
shotgunid
Only valid for SDP module, set to "NA".
Author(s)
Jeff Xia jeff.xia@mcgill.ca
McGill University, Canada
License: GNU GPL (>= 2)
xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.
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| FeatureCorrelation | R Documentation |
Main function to calculate correlation of all other feature to a given feature name
Description
This functions calculate correlation of all other feature to a given feature name. This is used in the Pattern Search analysis.
Usage
FeatureCorrelation(mbSetObj, dist.name, taxrank, feat)
Arguments
mbSetObj |
Input the name of the mbSetObj. |
dist.name |
Input the distance measure. Input "pearson" for Pearson R, "spearman" for Spearman rank correlation, and "kendall" for Kendall rank correlation. |
taxrank |
Character, input the taxonomic level to use. |
taxa |
If the pattern is defined by using a specific taxon, input the name of that taxa here. |
variable |
Input the name of the experimental factor. |
datatype |
If the data is marker gene, input "16S". If the data is metagenomic, use "metageno". |
shotfeat |
Only valid for SDP module, set to "null". |
shotgunid |
Only valid for SDP module, set to "NA". |
Author(s)
Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)
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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