RZooRoH (version 0.3.2.1)

zoorun: Run the ZooRoH model

Description

Apply the defined model on a group of individuals: parameter estimation, computation of realized autozygosity and homozygous-by-descent probabilities, and identification of HBD segments (decoding).

Usage

zoorun(
  zoomodel,
  zooin,
  ids = NULL,
  method = "opti",
  fb = TRUE,
  vit = TRUE,
  minr = 0,
  maxr = 1e+08,
  maxiter = 1000,
  convem = 1e-10,
  localhbd = FALSE,
  nT = 1
)

Value

The function return a zoores object with several slots accesses by the "@" symbol. The three main results are zoores@realized (the matrix with partitioning of the genome in different HBD classes for each individual), zoores@hbdseg (a data frame with identified HBD segments) and zoores@hbdp (a list of matrices with HBD probabilities per SNP and per class).

Here is a list with all the slots and their description:

1. zoores@nind the number of individuals in the analysis,

2. zoores@ids a vector containing the numbers of the analyzed individuals (their position in the data file),

3. zoores@mixc the (estimated) mixing coefficients per class for all individuals,

4. zoores@krates the (estimated) rates for the exponential distributions associated with each HBD or non-HBD class for all individuals,

5. zoores@niter the number of iterations for estimating the parameters (per individual),

6. zoores@modlik a vector containing the likelihood of the model for each individual,

7. zoores@modbic a vector containing the value of the BIC for each individual,

8. zoores@realized a matrix with estimated realized autozygosity per HBD class (columns) for each individual (rows). These values are obtained with the Forward-Backward algorithm - fb option),

9. zoores@hbdp a list of matrices with the local probabilities to belong to an underlying hidden state (computed for every class and every individual). Each matrix has one row per class and one column per snp. To access the matrix from individual i, use the brackets "[[]]", for instance zoores@hbdp[[i]],

10. zoores@hbdseg a data frame with the list of identified HBD segments with the Viterbi algorithm (the columns are the individual number, the chromosome number, the first and last SNP of the segment, the positions of the first and last SNP of the segment, the number of SNPs in the segment, the length of the segment, the HBD state of the segment),

11. zoores@optimerr a vector indicating whether optim ran with or without error (0/1),

12. zoores@sampleids is a vector with the names of the samples (when provided in the zooin object through the zoodata function).

Arguments

zoomodel

A valid zmodel object as defined by the zoomodel function. The model indicates whether rates of exponential distributions are estimated or predefined, the number of classes, the starting values for mixing coefficients and rates, the error probabilities. See "zoomodel" for more details.

zooin

A valid zdata object as obtained by the zoodata function. See "zoodata" for more details.

ids

An optional argument indicating the individual (its position in the data file) that must be proceeded. It can also be a vector containing the list of numbers that must be proceeded. By default, the model runs for all individuals.

method

Specifies whether the parameters are estimated by optimization with the L-BFGS-B method from the optim function (option method="opti", default value) or with the EM-algorithm (option method="estem"). When the EM algorithm is used, the Forward-Backward algorithm is run automatically (no need to select the fb option - see below). We recommend to set minr to 1 when using the EM algorithm. If the user doesn't want to estimate the parameters he must set method="no".

fb

A logical indicating whether the forward-backward algorithm is run (optional argument - true by default). The Forward-Backward algorithm estimates the local probabilities to belong to each HBD or non-HBD class. By default, the function returns only the HBD probabilities for each class, averaged genome-wide, and corresponding to the realized autozygosity associated with each class. To obtain HBD probabilities at every marker position, the option localhbd must be set to true (this generates larger outputs).

vit

A logical indicating whether the Viterbi algorithm is run (optional argument - true by default). The Viterbi algorithm performs the decoding (determining the underlying class at every marker position). Whereas the Forward-Backward algorithms provide HBD probabilities (and how confident a region can be declared HBD), the Viterbi algorithm assigns every marker position to one of the defined classes (HBD or non-HBD). When informativity is high (many SNPs per HBD segments), results from the Forward-Backward and the Viterbi algorithm are very similar. The Viterbi algorithm is best suited to identify HBD segments. To estimate realized inbreeding and determine HBD status of a position, we recommend to use the Forward-Backward algorithm that better reflects uncertainty.

minr

With optim and the reparametrized model (default), this indicates the minimum difference between rates of successive classes. With the EM algorithm, it indicates the minimum rate for a class. It is an optional argument set to 0. Adding such constraints might slow down the speed of convergence with optim and we recommend to run first optim without these constraints. With the EM algorithm, we recommend to use a value of 1.

maxr

With optim and the reparametrized model (default), this indicates the maximum difference between rates of successive classes. With the EM algorithm, it indicates the maximum rate for a class. It is an optional argument set to an arbitrarily large value (100000000). Adding such constraints might slow down the speed of convergence with optim and we recommend to run first optim without these constraints.

maxiter

Indicates the maximum number of iterations with the EM algorithm (optional argument - 1000 by default).

convem

Indicates the convergence criteria for the EM algorithm (optional argument / 1e-10 by default).

localhbd

A logical indicating whether the HBD probabilities for each individual at each marker are returned when using the EM or the Forward-Backward algorithm (fb option). This is an optional argument that is false by default.

nT

Indicates the number of threads used when running RZooRoH in parallel (optional argument - one thread by default).

Examples

# Start with a small data set with six individuals and external frequencies.
freqfile <- (system.file("exdata","typsfrq.txt",package="RZooRoH"))
typfile <- (system.file("exdata","typs.txt",package="RZooRoH"))
frq <- read.table(freqfile,header=FALSE)
typ <- zoodata(typfile,supcol=4,chrcol=1,poscol=2,allelefreq=frq$V1)
# Define a model with two HBD classes with rates equal to 10 and 100.
Mod3R <- zoomodel(K=3,base_rate=10)
# Run the model on all individuals.
typ.res <- zoorun(Mod3R, typ)
# Observe some results: likelihood, realized autozygosity in different
# HBD classes and identified HBD segments.
typ.res@modlik
typ.res@realized
typ.res@hbdseg
# Define a model with one HBD and one non-HBD class and run it.
Mod1R <- zoomodel(K=2,predefined=FALSE)
typ2.res <- zoorun(Mod1R, typ)
# Print the estimated rates and mixing coefficients.
typ2.res@krates
typ2.res@mixc
# Get the name and location of a second example file and load the data:
myfile <- (system.file("exdata","genoex.txt",package="RZooRoH"))
ex2 <- zoodata(myfile)
# Run RZooRoH to estimate parameters on your data with the 1 HBD and 1 non-HBD
# class (parameter estimation with optim).
my.mod1R <- zoomodel(predefined=FALSE,K=2,krates=c(10,10))
my.res <- zoorun(my.mod1R, ex2, fb = FALSE, vit = FALSE)
# The estimated rates and mixing coefficients:
my.res@mixc
my.res@krates
# Run the same model and run the Forward-Backward alogrithm to estimate
# realized autozygosity and the Viterbi algorithm to identify HBD segments:
my.res2 <- zoorun(my.mod1R, ex2)
# The table with estimated realized autozygosity:
my.res2@realized
# Run a model with 4 classes (3 HBD classes) and estimate the rates of HBD
# classes with one thread:
my.mod4R <- zoomodel(predefined=FALSE,K=4,krates=c(16,64,256,256))
my.res3 <- zoorun(my.mod4R, ex2, fb = FALSE, vit = FALSE, nT =1)
# The estimated rates for the 4 classes and the 20 individuals:
my.res3@krates
# Run a model with 5 classes (4 HBD classes) and predefined rates.
# The model is run only for a subset of four selected individuals.
# The parameters are estimated with the EM-algorithm, the Forward-Backward
# alogrithm is ued to estimate realized autozygosity and the Viterbi algorithm to
# identify HBD segments. One thread is used.
mix5R <- zoomodel(K=5,base=10)
my.res4 <- zoorun(mix5R,ex2,ids=c(7,12,16,18), method = "estem", nT = 1)
# The table with all identified HBD segments:
my.res4@hbdseg