# FIREVAT Constants
#
# Last revised date:
# February 19, 2019
#
# Authors:
# Andy Jinseok Lee (jinseok.lee@ncc.re.kr)
# Hyunbin Kim (khb7840@ncc.re.kr)
# Bioinformatics Analysis Team, National Cancer Center Korea
#' @title Constant
#' @description
#' PCAWG target mutational signatures reported to be unrelated to sequencing artifacts
#' @export
PCAWG.Target.Mutational.Signatures <- c("SBS1","SBS2","SBS3","SBS4","SBS5","SBS6",
"SBS7a","SBS7b","SBS7c","SBS7d","SBS8","SBS9",
"SBS10a","SBS10b","SBS11","SBS12","SBS13","SBS14",
"SBS15","SBS16","SBS17a","SBS17b","SBS18","SBS19",
"SBS20","SBS21","SBS22","SBS23","SBS24","SBS25","SBS26",
"SBS28","SBS29","SBS30","SBS31","SBS32","SBS33",
"SBS34","SBS35","SBS36","SBS37","SBS38","SBS39","SBS40",
"SBS41","SBS42","SBS44")
#' @title Constant
#' @description
#' PCAWG mutational signatures reported to be associated with sequencing artifacts
#' @export
PCAWG.Known.Sequencing.Artifact.Signatures <- c("SBS60")
#' @title Constant
#' @description
#' PCAWG mutational signatures reported to be associated with sequencing artifacts
#' @export
PCAWG.Possible.Sequencing.Artifact.Signatures <- c("SBS27","SBS43","SBS45","SBS46",
"SBS47","SBS48","SBS49","SBS50",
"SBS51","SBS52","SBS53","SBS54",
"SBS55","SBS56","SBS57","SBS58",
"SBS59")
#' @title Constant
#' @description
#' PCAWG mutational signatures reported to be associated with sequencing artifacts
#' @export
PCAWG.All.Sequencing.Artifact.Signatures <- c(PCAWG.Known.Sequencing.Artifact.Signatures,
PCAWG.Possible.Sequencing.Artifact.Signatures)
#' @title Constant
#' @description
#' PCAWG mutational signatures reported to be associated with sequencing artifacts
#' @export
PCAWG.Platinum.All.Technology.Related.Artifact.Signatures <- c("SBSR1",
"SBSR2",
"SBSR3",
"SBSR4",
"SBSR5",
"SBSR6",
"SBSR7",
"SBSR8",
"SBSR9")
#' @title Constant
#' @description
#' Hex codes for the mutation types (for plotting purposes)
#' @export
TriNuc.Mutation.Type.Hex.Colors <- c("#029ACE", # C>A
"#231F20", # C>G
"#CD5D5D", # C>T
"#B4B3B4", # T>A
"#9ACA3C", # T>C
"#D7BFD7") # T>G
#' @title Constant
#' @description
#' Chromosome names for FIREVAT.
#' Chromosome names should be given in the format of "chr" + chromosome number.
#' @export
Chromosome.Names <- c("chr1","chr2","chr3","chr4","chr5","chr6","chr7",
"chr8","chr9","chr10","chr11","chr12","chr13",
"chr14","chr15","chr16","chr17","chr18","chr19",
"chr20","chr21","chr22","chrX","chrY","chrM")
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