seq_query: query function

In ginnyintifa/SeqQuery:

Description

This function allows you to query a chormosome and a position

Usage

seq_query(query_chr, query_pos_start, query_pos_end, proc_tgf_path,
  proc_chr_path, codon_dictionary_path)

Arguments

query_chr	a string indicating the chromosome you want to query
query_pos_start	an integer indicating the starting position you are intersted
query_pos_end	an integer indicating the ending position you are intersted
proc_tgf_path	a string indicating the path to the processed tgf file (provided by the package,"tgf_df_CDS.Rds")
proc_chr_path	a string indicating the path to the directory of chromose fasta files (provided by the package,"chr*_seq.Rds")
codon_dictionary_path	a string indicating the path to the codon directory (provided by the package, "codon_dictionary.Rds")

Examples

getit = seq_query(query_chr = "chr1",
                  query_pos_start = 70000,
                  query_pos_end = 70000,
                  proc_tgf_path = "/data/ginny/GENCODE",
                  proc_chr_path = "/data/ginny/GENCODE/chromosomes",
                  codon_dictionary_path = "/data/ginny/GENCODE")

ginnyintifa/SeqQuery documentation built on May 18, 2019, 11:28 p.m.