inst/scripts/data4demo.R

In transbioZI/BioMMex: BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

#' @title An example of genome-wide DNA methylation data 
#'
#' @description Genome-wide DNA methylation data from the Illumina Infinium 
#' HumanMethylation27 BeadChip was downloaded from GSE38873. The data was then
#' corrected to account for the influence of potential confounders including 
#' age, batch, brain PMI and PH. For the demonstration, we only use a subset 
#' of the pre-processed data to reduce the runtime.
#' @docType data
#' @name methylData
#' @usage methylData
#' @format A data.frame with 26487 variables (26486 autosomal CpG probes and 
#' one label indicating case control status) and 20 samples (10 controls, 
#' 10 bipolar disorder patients). 
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38873}
#' @keywords datasets
NULL 


#' @title An example of pathway database
#'
#' @description A list of pathways with pathway (GO) IDs and their 
#' corresponding genes ("entrezID" is used) was processed using R library 
#' org.Hs.eg.db.
#' @docType data
#' @name goDB
#' @usage goDB
#' @format A list of pathways with bigger than 10 genes and less than 
#' 200 genes in each pathway. 
#' @source library(org.Hs.eg.db)
#' @keywords datasets
NULL 


#' @title An example of methylation data annotation file
#'
#' @description A pre-processed genomic annotation file for autosomal CpGs  
#' from the Illumina Infinium HumanMethylation27 BeadChip.
#' @docType data
#' @name cpgAnno
#' @usage cpgAnno
#' @format A data.frame with 4 variables ("ID", "chr", "entrezID", "symbol")
#'  and 26486 autosomal CpGs.
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38873}
#' @keywords datasets
NULL 


#' @title An example of pathway level data or stage-2 data.
#'
#' @description Self-prepared pathway level data (stage-2 data) generated by 
#' BioMMreconData() using the above examplar data sets: 'methylData', 'goDB' 
#' and 'cpgAnno'.
#' @docType data
#' @name stage2dataA
#' @usage stage2dataA
#' @format A data.frame with 51 variables. The first column is the label and 
#' the rest columns are 50 pathways.
#' @source Prepared by BioMMreconData() with 'methylData', 'goDB' 
#' and 'cpgAnno'. See BioMMreconData() for the details.
#' @keywords datasets
NULL