encGPC: Encoding barcode sequences using gap-pair compositional...

In funbarRF: Fungal Species Identification using DNA Barcode with Random Forest

Description

This function can be used for encoding the barcode sequences with gap-pair compositional features. This is an alternative function to seq_funbarRF and seq_funbarRF_manual functions.

Usage

encGPC (bar_seq)

Arguments

bar_seq

Barcode sequences of class DNAStringSet.

Details

The user has to supply the barcode sequences in FASTA format, the class of which must be of DNAString type. It can also be an object generated using read_seq_txt function.

Value

test	A dataframe of N rows and 96 columns, where N is the number of input sequences supplied by the user.

Author(s)

Prabina Kumar Meher, Division of Statistical Genetics,Indian Agricultural Statistics Research Institute, New Delhi-110012, INDIA

References

1. Li H. (2016). BioSeqClass: Classification for biological Sequences. R package version 1.32.0.

See Also

seq_funbarRF, seq_funbarRF_manual

Examples

data (fun_dat)
ms <- read_seq_txt (fun_dat$seq)[1:2]
res <- encGPC (ms)
head (res)

funbarRF documentation built on May 27, 2019, 5:03 p.m.