R/diffPt.R

In kojikoji/ptcomp: What the Package Does (One Line, Title Case)

##' Compare the LL for separated or merged model
##'
##' Calcualte LL for each treatment and merginalized data, and see the difference
##' @title calculateLLDiff
##' @param treatment1 character, first treatment
##' @param treatment2 character, second treatment
##' @param gene.vec character vec, gene names used in this comparison
##' @param ptcomp.df data frame, contain expression and annotation
##' @return diff.ll.df data frame, gene name, treatment1 ll, treatment2 ll, merged ll
##' @author Yasuhiro Kojima
##' @export
calculateLLDiff <- function(treatment1, treatment2, gene.vec, ptcomp.df, sparse.gp.res = 20){
  tr.gp.df.list <- purrr::map(
    list(tr1 = treatment1, tr2 = treatment2, merge = c(treatment1, treatment2)),
    function(treatment){
      calculateGPDf(
        gene.vec,
        dplyr::filter(ptcomp.df, treatment %in% !!treatment),
        sparse.gp.res = sparse.gp.res)
    })
  dplyr::inner_join(
    tr.gp.df.list$tr1,
    tr.gp.df.list$tr2,
    by = "gene",
    suffix = c(".tr1", ".tr2")) %>%
    dplyr::inner_join(
      tr.gp.df.list$merge) %>%
    dplyr::select(gene, ll.tr1, ll.tr2, ll) %>%
    dplyr::mutate(diff.ll = ll.tr1 + ll.tr2 - ll)
}


##' Permutate treatment labels
##'
##' @title permutateTreatment
##' @param ptcomp.df data frame, contain expression and annotation
##' @return permutated.ptcomp.df data frame, contain expression and annotation
##' @author Yasuhir Kojima
##' @export
permutateTreatment <- function(ptcomp.df){
  ptcomp.df$treatment <- sample(ptcomp.df$treatment)
  ptcomp.df
}