process_tmhmm {surfaltr} | R Documentation

## Create a data frame with the membrane locations of each amino acid in a sequence

### 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. The data frame includes columns with the transcript ID, membrane location, gene name, starting amino acid, and ending amino acid for a certain transcript. The first row for each transcript contains the overall length of the amino acid sequence.

### Usage

    process_tmhmm(topo, AA_seq)

### Arguments

`topo` | A data frame containing each transcript ID and the corresponding membrane location for each amino acid in its sequence formatted as a string.
`AA_seq` | A data frame containing the gene names, transcript IDs, APPRIS annotations, and protein sequences for each transcript.

### Value

A data frame containing the overall length and individual lengths of each section of the surface protein corresponding to a certain transcript.

[Package surfaltr version 1.0.0 Index]