read_metaphlan_table: A function to read MetaPhlAn 2.0 output file
In tvatanen/microbiomics: Microbiomics
Description
Usage
Arguments
Value
Author(s)
Description
This functions reads a MetaPhlAn 2.0 output file as an R data frame
Usage
1
2
read_metaphlan_table(filename, kingdom = "k__Bacteria", lvl = 7,
normalize = TRUE)
Arguments
filename
MetaPhlAn output file to be read
kingdom
to read: One of "k__Bacteria", "k__Viruses", "k__Eukaryota"
lvl
what level of taxonomy to read (default = 7, species)
normalize
logical to determine if the output data will be normalized
for each sample to sum up to unity (default: TRUE)
Value
a data frame with the MetaPhlAn results
Author(s)
Tommi Vatanen <tommivat@gmail.com>
tvatanen/microbiomics documentation built on Sept. 27, 2019, 7:29 a.m.
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Description Usage Arguments Value Author(s)
Description
This functions reads a MetaPhlAn 2.0 output file as an R data frame
Usage
1 2 | read_metaphlan_table(filename, kingdom = "k__Bacteria", lvl = 7,
normalize = TRUE)
|
Arguments
filename |
MetaPhlAn output file to be read |
kingdom |
to read: One of "k__Bacteria", "k__Viruses", "k__Eukaryota" |
lvl |
what level of taxonomy to read (default = 7, species) |
normalize |
logical to determine if the output data will be normalized for each sample to sum up to unity (default: TRUE) |
Value
a data frame with the MetaPhlAn results
Author(s)
Tommi Vatanen <tommivat@gmail.com>
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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