R/simDOdistr.R

In gammadnamix: Package for intepretation of quantitative DNA mixtures

#' @title simDOdistr
#' @author Oyvind Bleka <Oyvind.Bleka.at.fhi.no>
#' @description MCMC Allele dropout distribution sampler based on total number of alleles in an evidence.
#' @export
#' @details simDOdistr samples from the drop-out distribution based on total number of alleles in evidence under a specified prepositions. It returns if no samples was accepted in first iteration
#' @param totA Total number of allele-observations in evidence.
#' @param nC Number of contributors to assume in the preposition.
#' @param popFreq Population frequencies listed for each loci popFreq[[locname]]
#' @param refData List with alleles to condition on. ref[[locname]][[referencename]]=(A1,A2)
#' @param M is number of samples for each iteration.
#' @param minS is number of minimum accepted samples.
#' @param prC Assumed drop-in probability
#' @return Vector with accepted samples from the dropout distribution

simDOdistr= function(totA,nC,popFreq,refData=NULL,M=1e3,minS=2000,prC=0) {
 #totA - total number of alleles observed
 #nC - number of contributors (in each hypotheses)
 #popFreq - population frequencies for each loci
 
 #prC - drop-in probability
 primtall = c(2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 
        41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97, 101, 
        103, 107, 109, 113, 127, 131, 137, 139, 149, 151, 157, 
        163, 167, 173, 179, 181, 191, 193, 197, 199, 211, 223, 
        227, 229, 233, 239, 241, 251, 257, 263, 269, 271, 277, 
        281, 283, 293, 307, 311, 313, 317, 331, 337, 347, 349, 
        353, 359, 367, 373, 379, 383, 389, 397, 401, 409, 419, 
        421, 431, 433, 439, 443, 449, 457, 461, 463, 467, 479, 
        487, 491, 499, 503, 509, 521, 523, 541, 547, 557, 563, 
        569, 571, 577, 587, 593, 599, 601, 607, 613, 617, 619, 
        631, 641, 643, 647, 653, 659, 661, 673, 677, 683, 691, 
        701, 709, 719, 727, 733, 739, 743, 751, 757, 761, 769, 
        773, 787, 797, 809, 811, 821, 823, 827, 829, 839, 853, 
        857, 859, 863, 877, 881, 883, 887, 907, 911, 919, 929, 
        937, 941, 947, 953, 967, 971, 977, 983, 991, 997, 1009, 
        1013, 1019, 1021, 1031, 1033, 1039, 1049, 1051, 1061, 
        1063, 1069, 1087, 1091, 1093, 1097, 1103, 1109, 1117, 
        1123, 1129, 1151, 1153, 1163, 1171, 1181, 1187, 1193, 
        1201, 1213, 1217, 1223, 1229, 1231, 1237, 1249, 1259, 
        1277, 1279, 1283, 1289, 1291, 1297, 1301, 1303, 1307, 
        1319, 1321, 1327, 1361, 1367, 1373, 1381, 1399, 1409, 
        1423, 1427, 1429, 1433, 1439, 1447, 1451, 1453, 1459, 
        1471, 1481, 1483, 1487, 1489, 1493, 1499, 1511, 1523, 
        1531, 1543, 1549, 1553, 1559, 1567, 1571, 1579, 1583, 
        1597, 1601, 1607, 1609, 1613, 1619, 1621, 1627, 1637, 
        1657, 1663, 1667, 1669, 1693, 1697, 1699, 1709, 1721, 
        1723, 1733, 1741, 1747, 1753, 1759, 1777, 1783, 1787, 
        1789, 1801, 1811, 1823, 1831, 1847, 1861, 1867, 1871, 
        1873, 1877, 1879, 1889, 1901, 1907, 1913, 1931, 1933, 
        1949, 1951, 1973, 1979, 1987, 1993, 1997, 1999, 2003, 
        2011, 2017, 2027, 2029, 2039, 2053, 2063, 2069, 2081, 
        2083, 2087, 2089, 2099, 2111, 2113, 2129, 2131, 2137, 
        2141, 2143, 2153, 2161, 2179, 2203, 2207, 2213, 2221, 
        2237, 2239, 2243, 2251, 2267, 2269, 2273, 2281, 2287, 
        2293, 2297, 2309, 2311, 2333, 2339, 2341, 2347, 2351, 
        2357, 2371, 2377, 2381, 2383, 2389, 2393, 2399, 2411, 
        2417, 2423, 2437, 2441, 2447, 2459, 2467, 2473, 2477, 
        2503, 2521, 2531, 2539, 2543, 2549, 2551, 2557, 2579, 
        2591, 2593, 2609, 2617, 2621, 2633, 2647, 2657, 2659, 
        2663, 2671, 2677, 2683, 2687, 2689, 2693, 2699, 2707, 
        2711, 2713, 2719, 2729, 2731, 2741, 2749, 2753, 2767, 
        2777, 2789, 2791, 2797, 2801, 2803, 2819, 2833, 2837, 
        2843, 2851, 2857, 2861, 2879, 2887, 2897, 2903, 2909, 
        2917, 2927, 2939, 2953, 2957, 2963, 2969, 2971, 2999, 
        3001, 3011, 3019, 3023, 3037, 3041, 3049, 3061, 3067, 
        3079, 3083, 3089, 3109, 3119, 3121, 3137, 3163, 3167, 
        3169, 3181, 3187, 3191, 3203, 3209, 3217, 3221, 3229, 
        3251, 3253, 3257, 3259, 3271, 3299, 3301, 3307, 3313, 
        3319, 3323, 3329, 3331, 3343, 3347, 3359, 3361, 3371, 
        3373, 3389, 3391, 3407, 3413, 3433, 3449, 3457, 3461, 
        3463, 3467, 3469, 3491, 3499, 3511, 3517, 3527, 3529, 
        3533, 3539, 3541, 3547, 3557, 3559, 3571, 3581, 3583, 
        3593, 3607, 3613, 3617, 3623, 3631, 3637, 3643, 3659, 
        3671, 3673, 3677, 3691, 3697, 3701, 3709, 3719, 3727, 
        3733, 3739, 3761, 3767, 3769, 3779, 3793, 3797, 3803, 
        3821, 3823, 3833, 3847, 3851, 3853, 3863, 3877, 3881, 
        3889, 3907, 3911, 3917, 3919, 3923, 3929, 3931, 3943, 
        3947, 3967, 3989, 4001, 4003, 4007, 4013, 4019, 4021, 
        4027, 4049, 4051, 4057, 4073, 4079, 4091, 4093, 4099, 
        4111, 4127, 4129, 4133, 4139, 4153, 4157, 4159, 4177, 
        4201, 4211, 4217, 4219, 4229, 4231, 4241, 4243, 4253, 
        4259, 4261, 4271, 4273, 4283, 4289, 4297, 4327, 4337, 
        4339, 4349, 4357, 4363, 4373, 4391, 4397, 4409, 4421, 
        4423, 4441, 4447, 4451, 4457, 4463, 4481, 4483, 4493, 
        4507, 4513, 4517, 4519, 4523, 4547, 4549, 4561, 4567, 
        4583, 4591, 4597, 4603, 4621, 4637, 4639, 4643, 4649, 
        4651, 4657, 4663, 4673, 4679, 4691, 4703, 4721, 4723, 
        4729, 4733, 4751, 4759, 4783, 4787, 4789, 4793, 4799, 
        4801, 4813, 4817, 4831, 4861, 4871, 4877, 4889, 4903, 
        4909, 4919, 4931, 4933, 4937, 4943, 4951, 4957, 4967, 
        4969, 4973, 4987, 4993, 4999, 5003, 5009, 5011, 5021, 
        5023, 5039, 5051, 5059, 5077, 5081, 5087, 5099, 5101, 
        5107, 5113, 5119, 5147, 5153, 5167, 5171, 5179, 5189, 
        5197, 5209, 5227, 5231, 5233, 5237, 5261, 5273, 5279, 
        5281, 5297, 5303, 5309, 5323, 5333, 5347, 5351, 5381, 
        5387, 5393, 5399, 5407, 5413, 5417, 5419, 5431, 5437, 
        5441, 5443, 5449, 5471, 5477, 5479, 5483, 5501, 5503, 
        5507, 5519, 5521, 5527, 5531, 5557, 5563, 5569, 5573, 
        5581, 5591, 5623, 5639, 5641, 5647, 5651, 5653, 5657, 
        5659, 5669, 5683, 5689, 5693, 5701, 5711, 5717, 5737, 
        5741, 5743, 5749, 5779, 5783, 5791, 5801, 5807, 5813, 
        5821, 5827, 5839, 5843, 5849, 5851, 5857, 5861, 5867, 
        5869, 5879, 5881, 5897, 5903, 5923, 5927, 5939, 5953, 
        5981, 5987, 6007, 6011, 6029, 6037, 6043, 6047, 6053, 
        6067, 6073, 6079, 6089, 6091, 6101, 6113, 6121, 6131, 
        6133, 6143, 6151, 6163, 6173, 6197, 6199, 6203, 6211, 
        6217, 6221, 6229, 6247, 6257, 6263, 6269, 6271, 6277, 
        6287, 6299, 6301, 6311, 6317, 6323, 6329, 6337, 6343, 
        6353, 6359, 6361, 6367, 6373, 6379, 6389, 6397, 6421, 
        6427, 6449, 6451, 6469, 6473, 6481, 6491, 6521, 6529, 
        6547, 6551, 6553, 6563, 6569, 6571, 6577, 6581, 6599, 
        6607, 6619, 6637, 6653, 6659, 6661, 6673, 6679, 6689, 
        6691, 6701, 6703, 6709, 6719, 6733, 6737, 6761, 6763, 
        6779, 6781, 6791, 6793, 6803, 6823, 6827, 6829, 6833, 
        6841, 6857, 6863, 6869, 6871, 6883, 6899, 6907, 6911, 
        6917, 6947, 6949, 6959, 6961, 6967, 6971, 6977, 6983, 
        6991, 6997, 7001, 7013, 7019, 7027, 7039, 7043, 7057, 
        7069, 7079, 7103, 7109, 7121, 7127, 7129, 7151, 7159, 
        7177, 7187, 7193, 7207, 7211, 7213, 7219, 7229, 7237, 
        7243, 7247, 7253, 7283, 7297, 7307, 7309, 7321, 7331, 
        7333, 7349, 7351, 7369, 7393, 7411, 7417, 7433, 7451, 
        7457, 7459, 7477, 7481, 7487, 7489, 7499, 7507, 7517, 
        7523, 7529, 7537, 7541, 7547, 7549, 7559, 7561, 7573, 
        7577, 7583, 7589, 7591, 7603, 7607, 7621, 7639, 7643, 
        7649, 7669, 7673, 7681, 7687, 7691, 7699, 7703, 7717, 
        7723, 7727, 7741, 7753, 7757, 7759, 7789, 7793, 7817, 
        7823, 7829, 7841, 7853, 7867, 7873, 7877, 7879, 7883, 
        7901, 7907, 7919)

 pos = ceiling(log(1e-16)/log(prC))
 refvec <- list()
 locs <- names(popFreq) #loci to consider
 nL <- length(locs)
 uH <- rep(NA,nL) #number of unknowns
 for(loc in locs) {
  i <- which(locs==loc)
  refvec[[loc]] <- numeric()
  uH[i] <- nC
  if(!is.null(refData)) {
   refs <- refData[[loc]]
   for(j in 1:length(refs)) {
    refvec[[loc]] <- c(refvec[[loc]], refs[[j]])
   }
   uH[i] <- nC - length(refs) #number of unrestricted unknowns  
  }
 }
 if(any(uH<0)) { print("There was more references than contributors"); return(NULL) }

 #import LR-models elements
 prC_vec =  1-prC/(1-prC)
 if(pos>0) prC_vec <- c(prC_vec,prC^c(1:pos)) #dropout probabilities

 #Uknown numbers under hyps
 done<-FALSE
 cPrD_dist <- NULL

 while(!done) {
  aCount = rep(0,M)
  prDvec = runif(M) #sample prDs
  tmpcount = rep(0,M)
  for(loc in locs) {
   i <- which(locs==loc)
   freq <- popFreq[[loc]]
   freqN = as.numeric(names(freq))

   HRef = t(matrix(as.numeric(rep(refvec[[loc]],M)),ncol=M))
   HA = cbind(HRef,matrix(sample(freqN,2*M*uH[i],freq,replace=TRUE),nrow=M))

   #generate dropout:
   Z_h = matrix(runif(M*ncol(HA)),ncol=ncol(HA)) #get Z uniform samples
   Z_h = Z_h < prDvec #TRUE if dropped out

   #rename with primenumbers
   for(j in 1:length(freqN))  HA[HA==freqN[j]] = primtall[j]

   #Let droppouts get primenumber=1. These are always equal something
   for(j in 1:ncol(HA))  HA[ Z_h[,j] ,j] = 1

   #idea: Knows that product of different primes is unique
   #takes product of previous unique visited primers. Dropouts are also checked for!
   HA_tmp = HA[,1]
   cc_H = as.numeric(HA_tmp!=1) # counter: Don't count if dropout(equal 1)
   for(j in 2:ncol(HA)) { 
    equal = HA_tmp%%HA[,j]==0 | HA[,j]==1 #check if next primer is in product
    cc_H[!equal] = cc_H[!equal] + 1 #add to counter if not equal
    HA_tmp[!equal] = HA_tmp[!equal]*HA[!equal,j] #get product of primes
   }
  
   #generate dropin:
   #idea:
   # 1) generate number of dropouts
   # 2) For each size-number of contamination we generate prime numbers and
    #check the number of the prime-products to see if the cont-alleles are unique

   #samples number of contaminations in each case:
   ncontam = sample(0:pos,M,prob=prC_vec,replace=TRUE) #sample number of dropin
   contmax = max(ncontam)
   if(contmax>0) { #if any contanimation
    for(j in 1:contmax) { #for each size of contamination:
      sel = ncontam>=j
      if(sum(sel)>0) { #total number of contaminations
       prim = primtall[sample(1:length(freq),sum(sel),prob=freq,replace=TRUE)] #sample kind
       equal = HA_tmp[sel]%%prim==0
       cc_H[sel][!equal] = cc_H[sel][!equal] + 1 #add to counter if not equal
       HA_tmp[sel][!equal] = HA_tmp[sel][!equal]*prim[!equal] #get product of primes
     }
    } #end for each cont. size
   } #end if cont

   #count up uniques for loci 
   tmpcount = tmpcount  + cc_H 
  } #end for:iind #each loci

  cPrD_dist <- c(cPrD_dist,prDvec[tmpcount==totA])
  if(length(cPrD_dist)==0) return(cPrD_dist) #return if no samples was found in first iteration
  if(length(cPrD_dist)>=minS) done = TRUE
 } #end while
 return( cPrD_dist )
}