Profile-likelihood intervals for one single-cell bulk sample

Inverts the likelihood-ratio test for one coordinate of the profile log-likelihood. The two scales are concentrated out at every trial value. An endpoint that lands on a face is not a Wilks interval; use lrt_single_cell() for a boundary null.

Usage

confint_profile_single_cell(
  y,
  mean_signature_matrix,
  Sigma,
  level = 0.95,
  celltypes = colnames(mean_signature_matrix),
  variance = c("ml", "reml"),
  epsilon = 1e-08,
  itmax = 100L
)

Arguments

y

Bulk vector of length \(G\).

mean_signature_matrix

Reference mean, \(G\times J\).

Sigma

Cell-level covariances, \(G\times G\times J\).

level

Confidence level.

celltypes

Cell types to profile. Defaults to every column.

variance

"ml" (default) uses the \(\chi^2_1\) cut-off. "reml" uses \(G\log\{1+F_{1,\nu;1-\alpha}/\nu\}\) with \(\nu=G-J\), the exact cut-off of the profile likelihood ratio when a variance scale is profiled out of a linear model.

epsilon

Relative function and step tolerances passed to stats::nlminb().

itmax

Maximum number of iterations.

Value

A matrix with columns estimate, lower and upper.

See also

confint_single_cell(), lrt_single_cell()

Other decovart_inference: bootstrap_decovart(), bootstrap_single_cell(), boundary_diagnostics(), chi_bar_square_pvalue(), confint_decovart(), confint_ilr_backtransform(), confint_profile_decovart(), confint_single_cell(), equivariance_check_decovart(), fit_firth_decovart(), fit_firth_single_cell(), lrt_decovart(), lrt_single_cell(), multistart_decovart(), reference_bootstrap_decovart(), reference_bootstrap_single_cell(), restricted_mle_decovart(), restricted_mle_single_cell()

Examples

mu <- matrix(c(2, 0.2, 0.2, 2, 0.2, 3, 0.2, 3), nrow = 4)
colnames(mu) <- c("ct1", "ct2")
sigma <- array(rep(diag(0.05, 4), 2), c(4, 4, 2))
y <- 20 * drop(mu %*% c(0.7, 0.3)) + c(0.3, -0.2, 0.1, -0.1)
confint_profile_single_cell(y, mu, sigma)
#>     estimate     lower     upper
#> ct1 0.705328 0.7025836 0.7080680
#> ct2 0.294672 0.2919320 0.2974164