# Fungal Species Identification using DNA Barcode with Random Forest

## Documentation for package ‘funbarRF’ version 1.0.1

- DESCRIPTION file.

## Help Pages

data_barcode | Barcode sequences for five differet taxonomical entities i.e., Fish, Bat, Inga, Drosophila and Cypraeidae
encGPC | Encoding barcode sequences using gap-pair compositional features.
fun_dat | A dataset of 2726 fungal barcode sequences belonging to 1363 fungal species, where each species has exactly 2 sequence.
predict_test_funbarRF | Prediction of species label for the query fungal barcode sequences.
predict_train_funbarRF | Prediction of species labels for the out-of-bag (OOB) reference barcode sequence using Random Forest.
read_seq_txt | Conversion of DNA sequences of character types to DNAStringSet types.
seq_BOLD | Retrieveing barcode sequences from BOLD <URL: http://www.boldsystems.org/> database.
seq_funbarRF | Conversion of barcode sequences into numeric vectors based on gap pair compositions, with user supplied barcode sequences and species labels.
seq_funbarRF_BOLD | Conversion of barcode sequences into numeric feature vectors based on gap pair compositions, only for the sequences collected from BOLD database using the function 'seq_BOLD'.
seq_funbarRF_manual | Conversion of barcode sequences manually collected from BOLD database into numeric features based on gap pair compositions.
Unite | UNITE training dataset of 143723 sequences belonging to 9001 species.
WarcupRDS | Warcup training dataset which is trained with funbarRF.