get_tmhmm {surfaltr} | R Documentation

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

### Description

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

### Usage

    get_tmhmm(fasta_file_name, tmhmm_folder_name)

### Arguments

`fasta_file_name` | Name of .fasta file containing amino acid sequences
`tmhmm_folder_name` | Full path to folder containing installed TMHMM 2.0 software. This path should end in TMHMM2.0c

### 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 a folder called output within the working directory. Additionally, the file saves a copy of the returned data frame in csv format to the output folder in the working directory.

### Examples

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

[Package surfaltr version 1.0.0 Index]