R/data.R

In cgplab/PAMESdata: Precomputed lists of informative CpG sites and islands for PAMES package

#' Bladder Urothelial Carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"BLCA_sites"

#' Breast invasive carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"BRCA_sites"

#' Colon adenocarcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"COAD_sites"

#' Esophageal carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"ESCA_sites"

#' Head and Neck squamous cell carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"HNSC_sites"

#' Kidney renal clear cell carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"KIRC_sites"

#' Kidney renal papillary cell carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"KIRP_sites"

#' Liver hepatocellular carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"LIHC_sites"

#' Lung adenocarcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"LUAD_sites"

#' Lung squamous cell carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"LUSC_sites"

#' Pancreatic adenocarcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"PAAD_sites"

#' Prostate adenocarcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"PRAD_sites"

#' Thyroid carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"THCA_sites"

#' Uterine Corpus Endometrial Carcinoma
#'
#' A list of informative CpG sites to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Illumina BeadChip.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"UCEC_sites"

#-------------------------------------------------------------------------------
#' Bladder Urothelial Carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"BLCA_islands"

#' Breast invasive carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"BRCA_islands"

#' Colon adenocarcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"COAD_islands"

#' Esophageal carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"ESCA_islands"

#' Head and Neck squamous cell carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"HNSC_islands"

#' Kidney renal clear cell carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"KIRC_islands"

#' Kidney renal papillary cell carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"KIRP_islands"

#' Liver hepatocellular carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"LIHC_islands"

#' Lung adenocarcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"LUAD_islands"

#' Lung squamous cell carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"LUSC_islands"

#' Pancreatic adenocarcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"PAAD_islands"

#' Prostate adenocarcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"PRAD_islands"

#' Thyroid carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"THCA_islands"

#' Uterine Corpus Endometrial Carcinoma
#'
#' A list of informative CpG islands to be used with \code{\link[PAMES]{compute_purity}} from PAMES
#' package. Use with data from Bisulphite Sequencing after processing with
#' \code{\link[PAMES]{reduce_to_regions}}.
#'
#' @format A list of two vector of indexes (\code{hyper}- and \code{hypo}-methylated).
"UCEC_islands"

#-------------------------------------------------------------------------------
#' Bladder Urothelial Carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"BLCA_auc"

#' Breast invasive carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"BRCA_auc"

#' Colon adenocarcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"COAD_auc"

#' Esophageal carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"ESCA_auc"

#' Head and Neck squamous cell carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"HNSC_auc"

#' Kidney renal clear cell carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"KIRC_auc"

#' Kidney renal papillary cell carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"KIRP_auc"

#' Liver hepatocellular carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"LIHC_auc"

#' Lung adenocarcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"LUAD_auc"

#' Lung squamous cell carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"LUSC_auc"

#' Pancreatic adenocarcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"PAAD_auc"

#' Prostate adenocarcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"PRAD_auc"

#' Thyroid carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"THCA_auc"

#' Uterine Corpus Endometrial Carcinoma
#'
#' A vector of AUC computed with \code{\link[PAMES]{compute_AUC}} from PAMES
#' package. 
#'
#' @format A named numeric vector.
"UCEC_auc"