fasta_tidier: Converts a SeqFastadna object into a tidy dataframe.

In marcottelab/pepliner: MS Data Visualization

Description

Converts a SeqFastadna object into a tidy dataframe.

Usage

fasta_tidier(fasta_seqinr_object, annot = FALSE)

Arguments

fasta_seqinr_object	FASTA file read by seqinr::read.fasta from which the sequences will be extracted.
annot	If TRUE, extract sequence ID annotation into its own column
...	Unused extra arguments

Value

A tidy data.frame with one column for ID and one column for sequence.

ID	Sequence header from FASTA '>ID'
Sequence	Corresponding sequence, any bioalphabet (RNA/DNA/etc)
Annot	Full annotated FASTA header '>ID info|info|info'

Examples

seqinr::read.fasta function reads a FASTA file (format below) and returns a SeqFastadna object
   > GENENAME1
   atgctgacgta
   agctacagtat
   cagctactaag
seqinr_fasta_object <- seqinr::read.fasta("test.fasta")
fasta_tidier(seqinr_fasta_object)
fasta_tidier(seqinr_fasta_object, annot=TRUE)

marcottelab/pepliner documentation built on May 21, 2019, 8:05 a.m.