Function reference
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CARD_taxonomy
- CARD 3.1.4 and 1.1.3 aro_index hand curated and combine
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amr_raw_to_metagenomeseq
- Raw AMR files plus metadata to phyloseq object
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amr_raw_to_phyloseq
- Raw AMR files plus metadata to phyloseq object
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amr_read_taxonomy
- assign taxonomy for phylogenetic and AMR for each read
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epi2me2r
- epi2me2r.
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generate_amr_taxonomy
- Generates a taxonomy file for AMR count table
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generate_wimp_taxonomy()
- Generates a taxonomy file for WIMP court table using taxonomizr
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read_in_amr_files
- Convert raw AMR CSV files to data table
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read_in_wimp_files()
- Convert raw WIMP CSV files to data table
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wimp_raw_to_metagenomeseq()
- Raw WIMP files plus metadata to metagenomeseq object
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wimp_raw_to_phyloseq()
- Raw WIMP files plus metadata to phyloseq object