Package index • phylotypr

Functions

The functions needed to train the naive Bayesian classifier and run it on an unknown sequence

build_kmer_database(): Build kmer database

classify_sequence(): Classify 16S rRNA gene sequence fragment

filter_taxonomy(): Filter taxonomy

print_taxonomy(): Print taxonomy for an unknown sequence

read_fasta(): Read in a FASTA-formatted file containing DNA sequences

write_fasta(): Write to a FASTA-formatted file

read_taxonomy(): Read in taxonomy files

phylotypr_example(): Get path to phylotypr example

Datasets

Example reference sequences and taxonomy that can be used for practicing use of the package’s functions

trainset9_rdp trainset9_pds: RDP training set v9