scarcentralDB

Warning

This package is in early development and not yet ready for use

scarcentralDB is a database of molecular features associated with distinct processes of tumour development.

Installation

You can install the development version of scarcentralDB like so:

if(!require(pak)){ install.packages("pak") }
pak::pak("selkamand/scarcentralDB")

Quick Start

library(scarcentralDB)

# See all processes and scars in sigcentral
scarcentraldb <- scarcentral()
head(scarcentraldb)
#> [[1]]
#> ==============================================
#> Process:  Radiotherapy 
#> ==============================================
#> Description:  Damage caused by ionizing radiation therapy, typically seen in post-treatment tumors. 
#> 
#> Scars:  6 
#> Modalities:  DNA, RNA 
#> 
#> [[2]]
#> ==============================================
#> Process:  Methytransferase Dysfunction 
#> ==============================================
#> Description:  Global methylation disrupted by DNMT3A dysfunction. Common in Leukaemia. 
#> 
#> Scars:  2 
#> Modalities:  Methylation

For Developers

 # Creating two scars for Radiotherapy
 high_indel_burden <- new_scar(
   process = "Radiotherapy",
   scar_name = "High Indel Burden",
   marker_of = "Radiation Induced Damage",
   disease_specificity = "Pan-Cancer",
   diseases = "cancer",
   modality = "DNA",
   measurement = "INDEL / SBS ratio",
   description = "Higher number of INDELS driven by an increased burden of deletions.",
   experiment = "Analysis of 12 radiation-associated tumors compared to radiation-naive tumors",
   paper_url = "https://www.nature.com/articles/ncomms12605",
   specificity = "Low",
   specificity_tooltip = "Also observed in BRCA1/BRCA2 breast cancer.",
   sensitivity = "Moderate",
   sensitivity_tooltip = "All radiation tumors had values exceeding the median for their cancer type.",
   tool_name = "raDNA",
   tool_url = "https://github.com/selkamand/radna"
 )

 high_deletion_burden <- new_scar(
   process = "Radiotherapy",
   scar_name = "High Deletion Burden",
   marker_of = "Radiation Induced Damage",
   disease_specificity = "Pan-Cancer",
   diseases = "cancer",
   modality = "DNA",
   measurement = "Deletion / Insertion ratio",
   description = "Higher number of small deletions (1-100bp) particularly in regions of microhomology.",
   experiment = "Analysis of 12 radiation-associated tumors from 3 cancer types compared to radiation-naive tumors",
   paper_url = "https://www.nature.com/articles/ncomms12605",
   specificity = "Low",
   specificity_tooltip = "Also observed in BRCA1/BRCA2 breast cancer.",
   sensitivity = "Moderate",
   sensitivity_tooltip = "11/12 tumors had values exceeding the median for their cancer type.",
   tool_name = "raDNA",
   tool_url = "https://github.com/selkamand/radna"
 )

 # Create the Radiotherapy process object with two scars
 radiotherapy_process <- new_process(
   name = "Radiotherapy",
   description = "Damage caused by ionizing radiation therapy, typically seen in post-treatment tumors.",
   class = "exogenous",
   icon = "faRadiation",
   flip_vertical = FALSE,
   flip_horizontal = TRUE,
   scars = list(high_indel_burden, high_deletion_burden)
 )