align_prts {surfaltr} | R Documentation

## Get aligned amino acid sequences for gene transcripts

### Description

This function allows a user to specify genes of interest and subsequently receive a pdf of all the corresponding aligned amino acid sequences in pdf format.

### Usage

    align_prts(gene_names, data_file, if_aa = FALSE, organism = "human",
    temp = FALSE)

### Arguments

`gene_names` | Vector containing names of genes of interest (e.g. c(Crb1, Adgrl1))
`data_file` | Path to the input file
`if_aa` | Boolean value indicating if the input file contains amino acid sequence. TRUE indicates that sequences are present and FALSE indicates that only IDs are present.
`organism` | String indicating if the transcripts are from a human or a mouse
`temp` | Boolean indicating if the fasta file should be saved to the working directory or no

### Value

Nothing is returned.

### Note

Although the function returns nothing, it saves pdfs containing the aligned sequences to the working directory under a file labeled with the gene name.

### Examples

    tmhmm_folder_name <- "~/TMHMM2.0c"
    if (check_tmhmm_install(tmhmm_folder_name)) {
        align_prts(c("Crb1"), system.file("extdata", "crb1_example.csv",
            package = "surfaltr"
        ), TRUE, "mouse", TRUE)
    }

[Package surfaltr version 1.0.0 Index]