mergeGeneAnnotationFeature: Merge genome annotation together

In hongzhonglu/Yeastspot3D: Mutation mapping analysis with protein 3D structure for yeast

Description

This function was used to parse the genome annotation of s288c the result of this script is the base for all other analysis and should be run firstly firstly we need download gene annotation information from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/Saccharomyces_cerevisiae/reference/GCF_000146045.2_R64 which include:

1. GCF_000146045.2_R64_genomic.gbff

2. GCF_000146045.2_R64_cds_from_genomic.fna secondly we download the gene annotation information from SGD

3. s288_genome, which include the colnames: 1 "DBID" "systematic_name" "gene_standard_name" "gene_name" "locations_strand" "locations_start" "locations_end" "chromosome" "sequence" "sequnece_length" "protein_residue" "protein_length"

Usage

mergeGeneAnnotationFeature()

Value

A dataframe with the detailed gene annotation from NCBI and SGD database

Examples

# Once the essential datasets are prepared and put it under the directory- "xxx/data/"
# The function can be used as:
mergeGeneAnnotationFeature()

hongzhonglu/Yeastspot3D documentation built on March 28, 2020, 6:06 p.m.