AbsoluteAbundances: Translate the relative abundances into absolute abundances...
In katrikorpela/mare: Microbiota Analysis in R Easily
View source: R/AbsoluteAbundances.R
AbsoluteAbundances R Documentation
Translate the relative abundances into absolute abundances using total bacterial qPCR
Description
The function takes the taxonomic tables and a file with qPCR result (copies of 16S per 1g of sample) and calculates the absolute abundances of the 16S copies present in the sample. Optionally, also 16S rRNA gene copy number correction is done resulting in an estimate of absolute abundances of genomes.
Usage
TaxonomicTable(qPCR.file, qPCR.var, folder.name = "", copynumberDB = NULL)
Arguments
qPCR.file
Name of file in that contains a variable with the qPCR data. The samples should be in the same order as in the "readnumbers" file produced by ProcessReads.
qPCR.var
Name of the qPCR variable in the qPCR file.
folder.name
Name for the folder where the taxonomic tables are. Should be the same as the "folder.name" given to functions ProcessReads and TaxonomicTable.
copynumberDB
Optional. Path to a database with 16S rRNA gene copy number information for the bacterial taxa. Should have at least the variable "name", specifying the name of the organism and the variable "mean" specifying the mean copy number in the organism. See rrnDB for an example.
Author(s)
Katri Korpela
References
Stoddard S.F, Smith B.J., Hein R., Roller B.R.K. and Schmidt T.M. (2015) rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Research 2014; doi: 10.1093/nar/gku1201 [PMID:25414355]
katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.
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View source: R/AbsoluteAbundances.R
| AbsoluteAbundances | R Documentation |
Translate the relative abundances into absolute abundances using total bacterial qPCR
Description
The function takes the taxonomic tables and a file with qPCR result (copies of 16S per 1g of sample) and calculates the absolute abundances of the 16S copies present in the sample. Optionally, also 16S rRNA gene copy number correction is done resulting in an estimate of absolute abundances of genomes.
Usage
TaxonomicTable(qPCR.file, qPCR.var, folder.name = "", copynumberDB = NULL)
Arguments
qPCR.file |
Name of file in that contains a variable with the qPCR data. The samples should be in the same order as in the "readnumbers" file produced by ProcessReads. |
qPCR.var |
Name of the qPCR variable in the qPCR file. |
folder.name |
Name for the folder where the taxonomic tables are. Should be the same as the "folder.name" given to functions ProcessReads and TaxonomicTable. |
copynumberDB |
Optional. Path to a database with 16S rRNA gene copy number information for the bacterial taxa. Should have at least the variable "name", specifying the name of the organism and the variable "mean" specifying the mean copy number in the organism. See rrnDB for an example. |
Author(s)
Katri Korpela
References
Stoddard S.F, Smith B.J., Hein R., Roller B.R.K. and Schmidt T.M. (2015) rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Research 2014; doi: 10.1093/nar/gku1201 [PMID:25414355]
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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