MicPathmatch: MicPathmatch
In BiOFI: Feature Identification Between Metabolome and Microbiome in Disease and Health
MicPathmatch R Documentation
MicPathmatch
Description
A function is used to trace the affiliation between microbes (16S or Metagenome data) and functional pathways based on Kyoto Encyclopedia of Gene and Genomes (KEGG).
You can get two tables using this function.
One is a table including predicted detail next level strains and pathways of your own microbes, the other is a table including only your own microbes and corresponding pathways.
The format of microbe is like this:
k__XXX; p__XXX; c__XXX; o__XXX; f__XXX; g__XXX; s__XXX;
k means kingdom;
p means phylum;
c means class;
o means order;
f means family;
g means genus;
s means species.
Usage
MicPathmatch(microbes)
Arguments
microbes
A character vector containing the names of microbes.
Value
micmatch_res A list with two data frames, one contains strains, sub-strains and affiliated pathways and the other data frame does not contain strains or sub-strains.
Examples
MicPathmatch_res <- MicPathmatch(microbes = MicPathmatch.eg)
BiOFI documentation built on Sept. 22, 2022, 9:07 a.m.
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| MicPathmatch | R Documentation |
MicPathmatch
Description
A function is used to trace the affiliation between microbes (16S or Metagenome data) and functional pathways based on Kyoto Encyclopedia of Gene and Genomes (KEGG). You can get two tables using this function. One is a table including predicted detail next level strains and pathways of your own microbes, the other is a table including only your own microbes and corresponding pathways. The format of microbe is like this: k__XXX; p__XXX; c__XXX; o__XXX; f__XXX; g__XXX; s__XXX; k means kingdom; p means phylum; c means class; o means order; f means family; g means genus; s means species.
Usage
MicPathmatch(microbes)
Arguments
microbes |
A character vector containing the names of microbes. |
Value
micmatch_res A list with two data frames, one contains strains, sub-strains and affiliated pathways and the other data frame does not contain strains or sub-strains.
Examples
MicPathmatch_res <- MicPathmatch(microbes = MicPathmatch.eg)
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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