R/data.R

In lindberg-m/contextendR: Analyse genomic data with regard to sequence contexts

#' Genomic positions of single nucleotide variants in melanoma patients
#' from PCAWG
#' @format
#' \describe{
#'   \item{chrom}{chromosome}
#'   \item{pos}{position on chromosome}
#'   \item{ref}{reference nucleotide at genomic position}
#'   \item{alt}{nucleotide of mutated base at genomic position}
#' }
#' @source \url{https://dcc.icgc.org/api/v1/download\?fn\=/PCAWG/consensus_snv_indel/final_consensus_passonly.snv_mnv_indel.icgc.public.maf.gz}
"melanoma_mutations_promoters"

#' Promoter regions in hg19 saved as a GRanges object
#' @format 
#' \describe{
#'   \item{seqnames}{Chromosome names}
#'   \item{ranges}{Genomic positions}
#'   \item{strand}{strand, ignored}
#'   \item{name}{chromHMM region (only E2 included)}
#' }
#' @source \url{https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final/E059_15_coreMarks_segments.bed}
"promoters"