vc_test_asym: Computes variance component test statistic for longitudinal

In dearseq: Differential Expression Analysis for RNA-seq data through a robust variance component test

Description

This function computes an approximation of the variance component test based on the asymptotic distribution of a mixture of χ^{2}s using Davies method from davies

Usage

vc_test_asym(
  y,
  x,
  indiv = rep(1, nrow(x)),
  phi,
  w,
  Sigma_xi = diag(ncol(phi)),
  genewise_pvals = FALSE,
  homogen_traj = FALSE,
  na.rm = FALSE
)

Arguments

y	a numeric matrix of dim g x n containing the raw or normalized RNA-seq counts for g genes from n samples.
x	a numeric design matrix of dim n x p containing the p covariates to be adjusted for
indiv	a vector of length n containing the information for attributing each sample to one of the studied individuals. Coerced to be a factor.
phi	a numeric design matrix of size n x K containing the K longitudinal variables to be tested (typically a vector of time points or functions of time)
w	a vector of length n containing the weights for the n samples, corresponding to the inverse of the diagonal of the estimated covariance matrix of y.
Sigma_xi	a matrix of size K x K containing the covariance matrix of the K random effects corresponding to phi.
genewise_pvals	a logical flag indicating whether gene-wise p-values should be returned. Default is FALSE in which case gene set p-value is computed and returned instead.
homogen_traj	a logical flag indicating whether trajectories should be considered homogeneous. Default is FALSE in which case trajectories are not only tested for trend, but also for heterogeneity.
na.rm	logical: should missing values (including NA and NaN) be omitted from the calculations? Default is FALSE.

Value

A list with the following elements when the set p-value is computed:

• set_score_obs: the approximation of the observed set score

• set_pval: the associated set p-value

or a list with the following elements when gene-wise p-values are computed:

• gene_scores_obs: vector of approximating the observed gene-wise scores

• gene_pvals: vector of associated gene-wise p-values

See Also

davies

Examples

set.seed(123)

##generate some fake data
########################
n <- 100
r <- 12
t <- matrix(rep(1:(r/4)), 4, ncol=1, nrow=r)
sigma <- 0.4
b0 <- 1

#under the null:
b1 <- 0
#under the alternative:
#b1 <- 0.5
y.tilde <- b0 + b1*t + rnorm(r, sd = sigma)
y <- t(matrix(rnorm(n*r, sd = sqrt(sigma*abs(y.tilde))), ncol=n, nrow=r) +
      matrix(rep(y.tilde, n), ncol=n, nrow=r))
x <- matrix(1, ncol=1, nrow=r)

#run test
asymTestRes <- vc_test_asym(y, x, phi=cbind(t, t^2),
                           w=matrix(1, ncol=ncol(y), nrow=nrow(y)),
                           Sigma_xi=diag(2), indiv=1:r, genewise_pvals=TRUE)
plot(density(asymTestRes$gene_pvals))
quantile(asymTestRes$gene_pvals)

dearseq documentation built on Nov. 8, 2020, 5:49 p.m.