In kingyang728/genomicCoordinateConverter: Coordinate Converter

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

genomicCoordinateConverter

The goal of genomicCoordinateConverter is to provide functionalities supporting convert coordinate to amino acid information.The package contains 6 main converter functionalities:
genomic location (default genome: HG38), nucleotide exchange -> HUGO Symbol, transcript ID, position in primary transcript, exchanged amino acid
genomic location (default genome: HG38), nucleotide exchange -> HUGO Symbol, for all transcripts :transcript ID, position exchanged amino acid
genomic location (default genome: HG38) -> HUGO Symbol, list of all transcript ID
genomic location (default genome: HG38), nucleotide exchange -> HUGO symbol, exon number
transcript ID, position , target genome -> genomic location, triplet and number in triplet
Genomeversion, genomic location, taget genomeversion -> genomic location

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("kingyang728/genomicCoordinateConverter")

Example

This is a basic example which shows you how to convert genomic coordinate to target dataframe:

library(genomicCoordinateConverter)
## basic example code
#genomic location,  nucleotide exchange -> HUGO Symbol, transcript ID, position in primary transcript, exchanged amino acid
Coordinate_Covnerter1("chrX",48823056,48823056,"G","C")
#genomic location, nucleotide exchange -> HUGO Symbol, for all transcripts :transcript ID, position exchanged amino acid
Coordinate_Covnerter2("chrX",48823056,48823056,"G","C")
#genomic location -> HUGO Symbol, list of all transcript ID
Coordinate_Covnerter3("chrX",48823056,48823056)
#genomic location (default genome: HG38), nucleotide exchange ->  HUGO symbol, exon number
Coordinate_Covnerter4("chrX",48823056,48823056)
##transcript ID, position , target genome -> genomic location, triplet and number in triplet
##transcript id passed in should be ensembl transcript id like "ENST00000334136"
Coordinate_Covnerter5_2("ENST00000334136",2657)
#Genomeversion, genomic location, taget genomeversion -> genomic location
Coordinate_Covnerter6("chrX",45060024,45060024,"hg16","hg18")