run_phobius {surfaltr} | R Documentation

## Create a data frame with the membrane locations of each amino acid in a protein using Phobius

### Description

This function creates a data frame with columns containing transcript IDs and corresponding output from Phobius. The Phobius output includes a location for each amino acid, with O representing extracellular, M representing transmembrane, S representing signal, and i representing intracellular.

### Usage

    run_phobius(AA_seq, fasta_file_name)

### Arguments

`AA_seq` | A data frame outputted by the get_pairs function containing the gene names, transcript IDs, APPRIS annotations, and protein sequences for each transcript.
`fasta_file_name` | Path to fasta file containing amino acid sequences

### Value

A data frame containing each transcript ID and the corresponding membrane location for each amino acid in its sequence formatted as a string

### Note

In order for this function to work, there needs to be a .fasta file containing the amino acid sequences for each transcript called "AA.fasta" saved to the working directory. Additionally, the file saves a copy of the returned data frame in csv format to the working directory.

### Examples

    tmhmm_folder_name <- "~/TMHMM2.0c"
    if (check_tmhmm_install(tmhmm_folder_name)) {
        currwd <- getwd()
        AA_seq <- get_pairs(system.file("extdata", "crb1_example.csv",
            package = "surfaltr"
        ), TRUE, "mouse", TRUE)
        topo <- run_phobius(AA_seq, paste(getwd(), "/AA.fasta", sep = ""))
        setwd(currwd)
    }

[Package surfaltr version 1.0.0 Index]