View source: R/reshape_metaphlan2_result.R
reshape_metaphlan2_result | R Documentation |
This is a function that reshape metaphlan2 result for generating phyloseq object.
reshape_metaphlan2_result( metaphlan2_merged, remove_archaea = FALSE, remove_viruses = FALSE, level = "Species", abundance_filtering = 0.01, rescale = FALSE )
metaphlan2_merged |
Input a metaphlan2 merged result. |
remove_archaea |
Default is FALSE. If TRUE, remove Archea. |
remove_viruses |
Default is FALSE. If TRUE, remove Viruses. |
level |
Choose a taxonomy level to extract. The level name should be one of "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species". Default is "Species". |
abundance_filtering |
Set metaphlan results that lower than abundance_filtering to 0. Default is 0.01, metaphlan results are relative abundance. |
rescale |
Default is FALSE. If TRUE, rescale the metaphlan results after filtering. |
reshape_metaphlan2_result(metaphlan2_merged, level = "Species")
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