WhamFromBiobakery: Workflow Hub for Automated Metagenomic Exploration (WHAM!)
In zc1286/Wham: Workflow Hub for Automated Metagenomic Exploration (WHAM!)
Description
Usage
Arguments
Value
Examples
Description
R package allowing for exploratory analysis of metagenomics and metatranscriptomic data. Includes visualization and statistical analysis on the gene family and taxa level. This package is developped based on package ALDEx2.
Usage
1
WhamFromBiobakery(countData = NULL, colData = NULL, design = NULL)
Arguments
countData
a data frame or a matrix contains the counts generated from the biobakery process. The first three columns of the count table have to be "Acc","Taxa",and "Feature" respectively(case insensitive)
colData
metadata table contains experiment design with at least one column. The row number of coldata has to be equal to the columns of count table excluding the first three columns.
design
a formula expresses how the counts for each genes depend on the variables.e.g ~ group
Value
a WhamInput object contains countData, ColData, design, Taxainfo, FeatureInfo, TaxaTable
Examples
1
# see the vignette for more details
zc1286/Wham documentation built on May 14, 2021, 8 p.m.
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Description Usage Arguments Value Examples
Description
R package allowing for exploratory analysis of metagenomics and metatranscriptomic data. Includes visualization and statistical analysis on the gene family and taxa level. This package is developped based on package ALDEx2.
Usage
1 | WhamFromBiobakery(countData = NULL, colData = NULL, design = NULL)
|
Arguments
countData |
a data frame or a matrix contains the counts generated from the biobakery process. The first three columns of the count table have to be "Acc","Taxa",and "Feature" respectively(case insensitive) |
colData |
metadata table contains experiment design with at least one column. The row number of coldata has to be equal to the columns of count table excluding the first three columns. |
design |
a formula expresses how the counts for each genes depend on the variables.e.g ~ group |
Value
a WhamInput object contains countData, ColData, design, Taxainfo, FeatureInfo, TaxaTable
Examples
1 | # see the vignette for more details
|
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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