Defines functions .dropout_VDJ

# Drops out VDJ genes from germline gene list
# @param vdj_list List containing germline gene frequencies
# @param dropout_vdj named vector with numeric entry for V,D,J that denotes number of germline genes that should be dropped out
# @return VDJ list with modified germline gene frequencies.
# @examples
# dropout_VDJ(vdj_list, c(V=1,D=1,J=1))

  #allows dropout of V,D,J genes
  #specific or number
  #check whether V-genes should be dropped out
    #sample V-genes to dropout
    number_of_genes_to_drop <- dropout_vdj[["V"]]
    if(number_of_genes_to_drop < nrow(vdj_list$V)){
      rows_to_drop <- sample(1:nrow(vdj_list$V),number_of_genes_to_drop)
      #if number to drop out is larger than germline diversity dropout all but one gene.
      rows_to_drop <- sample(1:nrow(vdj_list$V),nrow(vdj_list$V)-1)
    #set frequency of chosen dropouts to zero and adjust overall frequency (to sum up to 1)
    vdj_list$V[rows_to_drop,"frequency"] <- 0
    vdj_list$V$frequency <- vdj_list$V$frequency*(1/sum(vdj_list$V$frequency))

  #repeat process for D and J gene
    number_of_genes_to_drop <- dropout_vdj[["D"]]
    if(number_of_genes_to_drop < nrow(vdj_list$D)){
      rows_to_drop <- sample(1:nrow(vdj_list$D),number_of_genes_to_drop)
      rows_to_drop <- sample(1:nrow(vdj_list$D),nrow(vdj_list$D)-1)
    vdj_list$D[rows_to_drop,"frequency"] <- 0
    vdj_list$D$frequency <- vdj_list$D$frequency*(1/sum(vdj_list$D$frequency))
    number_of_genes_to_drop <- dropout_vdj[["J"]]
    if(number_of_genes_to_drop < nrow(vdj_list$J)){
      rows_to_drop <- sample(1:nrow(vdj_list$J),number_of_genes_to_drop)
      rows_to_drop <- sample(1:nrow(vdj_list$J),nrow(vdj_list$J)-1)
    vdj_list$J[rows_to_drop,"frequency"] <- 0
    vdj_list$J$frequency <- vdj_list$J$frequency*(1/sum(vdj_list$J$frequency))


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immuneSIM documentation built on Sept. 27, 2019, 5:02 p.m.