R/calcDOdistr.R

In mastermix: Procedure for deconvolving, weight-evidence and database search using STR DNA mixtures

#' @title calcDOdistr
#' @author Oyvind Bleka <Oyvind.Bleka.at.fhi.no>
#' @description MCMC droppout sampler based on alleles in evidence.
#' @export
#' @details calcDOdistr takes in models under Hp and Hd and samples from the drop-out distribution based on total number of alleles in evidence.
#' @param LRopt Model object returned by getLRopt function of GUI.
#' @param sample is name of sample to be considered in the calculation.
#' @param M is number of samples for each iteration.
#' @param minS is number of minimum accepted samples.
#' @param hdOnly is boolean wheter hp hypothesis is also considered.
#' @return List with sample-elements for each hypothesis.


calcDOdistr = function(LRopt,sample,M=1e3,minS=500,hdOnly=FALSE) {
 #LRopt is a LR-model object from LRcalculation having certain elements in list
 #sample is index of what mixture to consider
 #hdOnly boolean consider hd only
 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)  

 #import LR-models elements
 prC = LRopt$DIprob #dropout
 pos = ceiling( log(1e-16)/log(prC) )  #want low prob to achieve many dropouts
 if(pos<=0)  prC_vec = 1
 if(pos>0) prC_vec =  c(1-prC/(1-prC),prC^c(1:pos)) #dropout probabilities
 if(!hdOnly) uHp = LRopt$uHp 
 uHd = LRopt$uHd
 locs <- names(LRopt$LRfit)

 totA <- 0
 for(loc in locs) {
  totA <- totA + length(LRopt$LRfit[[loc]]$evidList[[sample]])
 }
 print(paste0("Total alleles in mixture=",totA))
 #Uknown numbers under hyps
 done<-FALSE
 cPrD_dist_hp <- numeric()
 cPrD_dist_hd <- numeric()
 while(!done) {
  if(!hdOnly) aCount_hp = rep(0,M)
  aCount_hd = rep(0,M)
  prDvec = runif(M) #sample prDs
  if(!hdOnly) tmpcount_hp = rep(0,M)
  tmpcount_hd = rep(0,M)
  for(loc in locs) {
   nA <- length(LRopt$LRfit[[loc]]$evidList[[sample]])
   if(nA==0) next
   freq <- LRopt$LRfit[[loc]]$freq #use all frequencies in population
   freqN = as.numeric(names(freq))

   if(!hdOnly) HpRef = t(matrix(as.numeric(rep(LRopt$LRfit[[loc]]$refHp,M)),ncol=M))
   HdRef = t(matrix(as.numeric(rep(LRopt$LRfit[[loc]]$refHd,M)),ncol=M))
   if(!hdOnly) HpA = cbind(HpRef,matrix(sample(freqN,2*M*uHp,freq,replace=TRUE),nrow=M))
   HdA = cbind(HdRef,matrix(sample(freqN,2*M*uHd,freq,replace=TRUE),nrow=M))

   #generate dropout:
   if(!hdOnly) Z_hp = matrix(runif(M*ncol(HpA)),ncol=ncol(HpA)) #get Z uniform samples
   Z_hd = matrix(runif(M*ncol(HdA)),ncol=ncol(HdA)) #get Z uniform samples
   if(!hdOnly) Z_hp = Z_hp < prDvec #TRUE if dropped out
   Z_hd = Z_hd < prDvec #TRUE if dropped out

   #rename 
   for(i in 1:length(freqN)) {
    if(!hdOnly) HpA[HpA==freqN[i]] = primtall[i]
    HdA[HdA==freqN[i]] = primtall[i]
   }

   #Let droppouts get primenumber=1. These are always equal something
   if(!hdOnly) {
    for(i in 1:ncol(HpA)) HpA[ Z_hp[,i] ,i] = 1
   }
   for(i in 1:ncol(HdA)) HdA[ Z_hd[,i] ,i] = 1

   #idea: Knows that product of different primes is unique
   #takes product of previous unique visited primers. Dropouts are also checked for!
   if(!hdOnly) HpA_tmp = HpA[,1]
   HdA_tmp = HdA[,1]
   if(!hdOnly) cc_Hp = as.numeric(HpA_tmp!=1) # counter: Don't count if dropout(equal 1)
   cc_Hd = as.numeric(HdA_tmp!=1) # counter: Don't count if dropout(equal 1)
   #Hp:
   if(!hdOnly) {
    for(i in 2:ncol(HpA)) { 
     equal = HpA_tmp%%HpA[,i]==0 | HpA[,i]==1 #check if next primer is in product
     cc_Hp[!equal] = cc_Hp[!equal] + 1 #add to counter if not equal
     HpA_tmp[!equal] = HpA_tmp[!equal]*HpA[!equal,i] #get product of primes
    }
   }
   #Hd:
   for(i in 2:ncol(HdA)) { 
    equal = HdA_tmp%%HdA[,i]==0 | HdA[,i]==1#check if next primer is in product
    cc_Hd[!equal] = cc_Hd[!equal] + 1 #add to counter if not equal
    HdA_tmp[!equal] = HdA_tmp[!equal]*HdA[!equal,i] #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 drop-in for a given locus:
   #Masking alleles are possible drop-in
   ncontam_hp <- 0
   if(!hdOnly) ncontam_hp = sample(0:pos,M,prob=prC_vec,replace=TRUE) #sample number of cont
   ncontam_hd = sample(0:pos,M,prob=prC_vec,replace=TRUE) #sample number of cont
   contmax = max(c(ncontam_hp,ncontam_hd))
   if(contmax>0) { #if any contanimation
    for(i in 1:contmax) { #for each size of contamination:
     if(!hdOnly) {
      #Hp:
      sel_hp = ncontam_hp>=i
      if(sum(sel_hp)>0) { #total number of contaminations
       prim_hp = primtall[sample(1:length(freq),sum(sel_hp),prob=freq,replace=TRUE)] #sample kinds
       equal = HpA_tmp[sel_hp]%%prim_hp==0
       cc_Hp[sel_hp][!equal] = cc_Hp[sel_hp][!equal] + 1 #add to counter if not equal
       HpA_tmp[sel_hp][!equal] = HpA_tmp[sel_hp][!equal]*prim_hp[!equal] #get product of primes
      }
     }
     #Hd:
     sel_hd = ncontam_hd>=i
     if(sum(sel_hd)>0) {
      prim_hd = primtall[sample(1:length(freq),sum(sel_hd),prob=freq,replace=TRUE)] #sample kind
      equal = HdA_tmp[sel_hd]%%prim_hd==0
      cc_Hd[sel_hd][!equal] = cc_Hd[sel_hd][!equal] + 1 #add to counter if not equal
      HdA_tmp[sel_hd][!equal] = HdA_tmp[sel_hd][!equal]*prim_hd[!equal] #get product of
     }
    } #end for each cont. size
   } #end if cont

   #count up uniques for loci 
   if(!hdOnly) tmpcount_hp = tmpcount_hp + cc_Hp 
   tmpcount_hd = tmpcount_hd + cc_Hd 

  } #end for:iind #each loci
  cPrD_dist_hd <- c(cPrD_dist_hd,prDvec[tmpcount_hd==totA])
  if(!hdOnly) {
   cPrD_dist_hp <- c(cPrD_dist_hp,prDvec[tmpcount_hp==totA])
   if(length(cPrD_dist_hp)==0) stop(paste("No samples found in",M,"samples under Hp"))
   if(length(cPrD_dist_hp)>=minS & length(cPrD_dist_hd)>=minS) done=TRUE
  }
  if(length(cPrD_dist_hd)==0) stop(paste("No samples found in",M,"samples under Hd"))
  if(hdOnly && length(cPrD_dist_hd)>=minS) done=TRUE

  print(paste("hp-samples:",length(cPrD_dist_hp)," | hd-samples:",length(cPrD_dist_hd),sep=""))
 } #end while
 return( list(hpsamples=cPrD_dist_hp,hdsamples=cPrD_dist_hd) )
}