align_org_prts {surfaltr} | R Documentation

## Get aligned amino acid sequences for gene transcripts from multiple organisms

### Description

This function allows a user to specify genes of interest and subsequently receive a pdf of all the corresponding aligned human and mouse amino acid sequences. In order for this to work, transcripts for the same genes from both organisms need to be provided in separate files.

### Usage

    align_org_prts(gene_names, hs_data_file, mm_data_file, if_aa = FALSE,
    temp = FALSE)

### Arguments

`gene_names` | Vector containing names of genes of interest (e.g. c("Crb1", "Adgrl1"))
`hs_data_file` | Path to the input file containing the human transcripts
`mm_data_file` | Path to the input file containing the mouse transcripts
`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.
`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. It's also important to note that although the gene names will be standardized to be fully capitalized, this may not match with the case of the gene name for some organisms.

### Examples

    tmhmm_folder_name <- "~/TMHMM2.0c"
    if (check_tmhmm_install(tmhmm_folder_name)) {align_org_prts( c("IGSF1"),
    system.file("extdata", "hpa_example.csv", package = "surfaltr"),
    system.file("extdata", "hpa_mouse_example.csv",
    package = "surfaltr"),
    FALSE, TRUE)}

[Package surfaltr version 1.0.0 Index]