# Function to calculate the expected number of read counts for a gene based
# on labeled and unlabeled RNA amounts, the length of the gene, and sequencing
# depth and cross contamination rate of the sample
#
# Author: demel
###############################################################################
#' Implementation of Equation 1 and 2 -> get alpha and beta
#'
#' @param L length Li of genes
#' @param labeled.amount labeled amount of gene i in sample j = alpha_ij
#' @param unlabeled.amount unlabeled amount of gene i in sample j = beta_ij
#' @param N number of cells
#' @param epsilon cross contamination rate (=1 in total samples)
#' @param sigma sequencing depth in sample j (independent whether total or
#' labeled sample)
#' @return expected counts
#'
#' @author Carina Demel
#' @export
getExpectedCounts <- function(
L,
labeled.amount,
unlabeled.amount,
N,
epsilon,
sigma
){
exp.counts = N * L *
t(sigma * (t(labeled.amount) + epsilon * t(unlabeled.amount)))
return(exp.counts)
}
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