qtl2pleio (version 1.2.3)

boot_pvl: Perform bootstrap sampling and calculate test statistics for each bootstrap sample

Description

Create a bootstrap sample, perform multivariate QTL scan, and calculate LRT statistic

Usage

boot_pvl(probs, pheno, addcovar = NULL, kinship = NULL,
  start_snp = 1, n_snp, pleio_peak_index, nboot_per_job = 1,
  max_iter = 10000, max_prec = 1/1e+08, n_cores = 1)

Arguments

probs

founder allele probabilities three-dimensional array for one chromosome only (not a list)

pheno

n by d matrix of phenotypes

addcovar

n by c matrix of additive numeric covariates

kinship

a kinship matrix, not a list

start_snp

positive integer indicating index within probs for start of scan

n_snp

number of (consecutive) markers to use in scan

pleio_peak_index

positive integer index indicating genotype matrix for bootstrap sampling. Typically acquired by using `find_pleio_peak_tib`.

nboot_per_job

number of bootstrap samples to acquire per function invocation

max_iter

maximum number of iterations for EM algorithm

max_prec

stepwise precision for EM algorithm. EM stops once incremental difference in log likelihood is less than max_prec

n_cores

number of cores to use when calling `scan_pvl`

Value

numeric vector of (log) likelihood ratio test statistics from `nboot_per_job` bootstrap samples

Details

Performs a parametric bootstrap method to calibrate test statistic values in the test of pleiotropy vs. separate QTL. It begins by inferring parameter values at the `pleio_peak_index` index value in the object `probs`. It then uses these inferred parameter values in sampling from a multivariate normal distribution. For each of the `nboot_per_job` sampled phenotype vectors, a two-dimensional QTL scan, starting at the marker indexed by `start_snp` within the object `probs` and extending for a total of `n_snp` consecutive markers. The two-dimensional scan is performed via the function `scan_pvl`. For each two-dimensional scan, a likelihood ratio test statistic is calculated. The outputted object is a vector of `nboot_per_job` likelihood ratio test statistics from `nboot_per_job` distinct bootstrap samples.

References

Knott SA, Haley CS (2000) Multitrait least squares for quantitative trait loci detection. Genetics 156: 899<U+2013>911.

Walling GA, Visscher PM, Haley CS (1998) A comparison of bootstrap methods to construct confidence intervals in QTL mapping. Genet. Res. 71: 171<U+2013>180.

Examples

# NOT RUN {
probs_pre <- rbinom(n = 100 * 10, size = 1, prob = 1 / 2)
probs <- array(data = probs_pre, dim = c(100, 1, 10))
s_id <- paste0('s', 1:100)
rownames(probs) <- s_id
colnames(probs) <- 'A'
dimnames(probs)[[3]] <- paste0('Marker', 1:10)
# define Y
set.seed(2018-12-29)
Y_pre <- runif(200)
Y <- matrix(data = Y_pre, nrow = 100)
rownames(Y) <- s_id
colnames(Y) <- paste0('t', 1:2)
addcovar <- matrix(c(runif(99), NA), nrow = 100, ncol = 1)
rownames(addcovar) <- s_id
colnames(addcovar) <- 'c1'
kin <- diag(100)
rownames(kin) <- s_id
colnames(kin) <- s_id
Y2 <- Y
Y2[1, 2] <- NA
boot_pvl(probs = probs, pheno = Y, kinship = kin,
        start_snp = 1, n_snp = 10, pleio_peak_index = 10, nboot_per_job = 1)
boot_pvl(probs = probs, pheno = Y2, kinship = kin,
        start_snp = 1, n_snp = 10, pleio_peak_index = 10, nboot_per_job = 2)


# }