R/generateIntervalMidPoints.R

In rohan-shah/mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

#' @title Specify interval midpoints
#' @description Specify interval midpoints
#' @details Some functions, such as \code{imputeFounders} and \code{computeGenotypeProbabilities}, take in a set of genetic positions as one of the inputs. This function is an easy way to specify the midpoint of every marker interval. 
#' 
#' Note that you don't have to explicitly evaluate this function, it can be passed in directly (see examples). 
#' @param object The object of class \code{mpcrossMapped} from which to take the interval midpoints. 
#' @return A function which can be applied to an object of class \code{mpcrossMapped} by \code{imputeFounders} or \code{computeGenotypeProbabilities}. 
#' @examples
#' data(simulatedFourParentData)
#' #Create object that includes the correct map
#' mapped <- new("mpcrossMapped", simulatedFourParentData, map = simulatedFourParentMap)
#' #Estimate IBD genotypes at all the markers, and marker midpoints
#' imputed <- imputeFounders(mapped, errorProb = 0.02, 
#' 	extraPositions = generateIntervalMidPoints(mapped))
#' #Alternatively we can explicitly evaluate the function. This is identical to above.
#' imputed <- imputeFounders(mapped, errorProb = 0.02, 
#' 	extraPositions = generateIntervalMidPoints)
#' @export
generateIntervalMidPoints <- function(object)
{
	if(!is(object, "mpcrossMapped"))
	{
		stop("Input must be an object of class mpcrossMapped")
	}
	result <- lapply(as.list(names(object@map)), function(chrName)
		{
			uniquePositions <- unique(object@map[[chrName]])
			midPoints <- (head(uniquePositions, -1) + tail(uniquePositions, -1))/2
			names(midPoints) <- paste0("Chr", chrName, "Interval", 1:length(midPoints))
			midPoints
		})
	names(result) <- names(object@map)
	result
}