genome_treatment: Virus Variant Identifier(VVI)

This is a R pacakge including some tools to treat aligned genome sequence.

To acess them, you can try

 library(devtools)
 install_github("wuaipinglab/genome_treatment/findout")
 library(findout)
 ?findout::findout_mutation()
 ?findout::findout_NTtoAA()

1. findout

This is developed for SARS-CoV-2.

Now the available package is:

1.1 findout_mutation (depending on tidyr, stringr)

Description: When you try to call INDEL or SNP from a very large and already aligned geonome sequences on your local system, I will recommend you to use it. To use it try:

  findout_mutation(filename, key_pattern)

Parameters:

filename: The file name of your aligned sequences.

key_pattern: An unique pattern in your refference sequence in the above aligned file, such as a EPI id.

As a quality control, sequences will be removed with more than 15 "N" or 50 other degenerate bases like "R".

1.2 findout_NTtoAA (depending on ape, dplyr)

 Description: If you have la list of nucleotide mutation and want to figure out which protein located on or whether lead to a non-synonymous mutation or not, I would like to introduce this package to you.
 
 To use it try: 
   
  findout_NTtoAA(Seq_fasta, ORF_table_file, SNP_table_file)

Parameters:

Seq_fasta: reference sequence, make sure this seqeunce has the closest evolution distance to your input.

ORF_table_file: Address to a csv file list a Open Reading Frame Table to your reference sequence.

SNP_table_file: Address to a csv file list the SNP intresting you, such as A21222T. It should be in nucleotide.

ORFStartCol = "Start": The colname of the Start site in ORF_table_file

ORFEndCol = "End": The colname of the End site in ORF_table_file

ORFGeneCol="Gene": The colname of the Gene name in ORF_table_file

SNP = "SNP": The colname of the SNP in SNP_table_file

Good Luck