align_prts: Get aligned amino acid sequences for gene transcripts

In EliLillyCo/surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

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)
}

EliLillyCo/surfaltr documentation built on May 3, 2022, 10:12 a.m.