R/applySimulatePanel.R

In acc-bioinfo/TMBleR: Tumor Mutational Burden Quantification From Gene Panels And WES

#' Downsample a whole exome sequencing (WES) dataset to a subset only containing
#' genes targeted in the panel
#'
#' This function calls the simulatePanel function on a list of inputs and for 
#' each element of the list it generates a subset of a whole exome sequencing 
#' dataset which only includes the genes of a given gene panel. This subset may 
#' then be used to simulate panel-based TMB quantification.
#'
#' @param WES a list generated by applyFilters or applyInputToTMB with variants,
#' filter, design and sample elements.
#' @param WES.design a \code{GRanges} object containing WES sequencing design. 
#' Used to remove off target mutations
#' @param panel.design a \code{GRanges} object containing sequencing design of
#' the panel tyou want to simuate. Used to subset WES.
#' @param assembly human genome assembly: "hg19" or "hg38"
#'
#' @return Returns a list of lists (one for each element of the input list). Each
#' list contains variants, filter, design and sample elements. The variants element 
#' is a \code{GRanges} object containing variants from the simulated panel, which
#' is only those variants from WES falling in the regions targeted by the panel
#'
#' @examples
#'
#' ## Read design
#' # Load the design of the WES
#' data(ExampleWESdesign)
#'
#' # Load the design of the gene panel that you want to simulate
#' data(ExamplePaneldesign)
#'
#' # Load input to applySimulatePanel function
#' data(vcfs_NoCancer_ForPanel)
#'
#' # Subset WES dataset, provided as GRanges object so that it will only contain
#' # variants in the regions targeted by the panel you want to simulate
#' SimulatedPanel_NoCancer <- applySimulatePanel(WES = vcfs_NoCancer_ForPanel
#'	, WES.design = ExampleWESdesign
#'	, panel.design= ExamplePaneldesign 
#'	, assembly = "hg19")
#'
#' @author Laura Fancello
#'
#' @export
applySimulatePanel <- function(WES, WES.design, panel.design, assembly){
    
    simulatedPanel=lapply(WES
                          , simulatePanel
                          , WES.design
                          , panel.design
                          , assembly)
    
    return(simulatedPanel)
    }