scale_and_visualize: Function to perform individual_scale function AND...
In econtijoch/Biomass-Workflow: Microbial Density Data Generation and Analysis Tools
Description
Usage
Arguments
Value
Description
Function to perform individual_scale function AND vizualization functon
Usage
1
scale_and_visualize(biom_file, metadata_file, taxonomy_file, filter = 0)
Arguments
biom_file
.biom table in rhdf5 format. It is wise to use a pre-filtered table (for example, de-duplicated)
metadata_file
the mapping file used in QIIME to split your sequencing library (must include microbial biomass data)
taxonomy_file
a file containing taxonomy (e.g. output from assign_taxonomy.py in QIIME, or greengenes taxonomy)
filter
OPTIONAL: minimum relative abundance to filter from data
Value
a list containing OTU tables with and without taxonomy (at each given depth), both scaled and unscaled (the output is a list of lists).
econtijoch/Biomass-Workflow documentation built on May 15, 2019, 7:59 p.m.
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Description Usage Arguments Value
Description
Function to perform individual_scale function AND vizualization functon
Usage
1 | scale_and_visualize(biom_file, metadata_file, taxonomy_file, filter = 0)
|
Arguments
biom_file |
.biom table in rhdf5 format. It is wise to use a pre-filtered table (for example, de-duplicated) |
metadata_file |
the mapping file used in QIIME to split your sequencing library (must include microbial biomass data) |
taxonomy_file |
a file containing taxonomy (e.g. output from assign_taxonomy.py in QIIME, or greengenes taxonomy) |
filter |
OPTIONAL: minimum relative abundance to filter from data |
Value
a list containing OTU tables with and without taxonomy (at each given depth), both scaled and unscaled (the output is a list of lists).
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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