align_org_prts: Get aligned amino acid sequences for gene transcripts from...

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

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)}

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