get_aas: Create fasta file containing amino acid sequences based on...

In EliLillyCo/surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Create fasta file containing amino acid sequences based on user sequences

Description

This function creates a fasta file with the transcript ID followed by the amino acid sequence for all inputted and associated primary transcripts. The file is organized so that all transcripts from a gene are next to each other. The function also returns a final table containing the gene names, transcript IDs, APPRIS annotations, and amino acid sequences for each transcript

Usage

get_aas(final_pairs, temp = FALSE)

Arguments

final_pairs	A data frame containing gene names, transcript IDs, amino acid sequences, and APPRIS annotations for all inputted data and its corresponding primary transcripts.
temp	Boolean indicating if the fasta file should be deleted after the function finishes running or not. Recommended to always be set to FALSE.

Value

A data frame containing the gene names, transcript IDs, APPRIS annotations, and protein sequences for each transcript.

Note

This function also creates a fasta file containing the transcript IDs and associated amino acid sequences in the root directory.

EliLillyCo/surfaltr documentation built on May 3, 2022, 10:12 a.m.