ICskat {ICSKAT}

ICSKAT.R

Description

Calculate the test statistic and p-value for interval-censored SKAT.

Usage

ICskat(
  left_dmat,
  right_dmat,
  lt,
  rt,
  obs_ind,
  tpos_ind,
  gMat,
  null_beta,
  Itt,
  pvalue = TRUE
)

Arguments

left_dmat

n*(p+nknots+2) design matrix for left end of interval.

right_dmat

n*(p+nknots+2) design matrix for right end of interval.

lt

n*1 vector of left side of interval times.

rt

n*1 vector of right side of interval times.

obs_ind

n*1 vector of whether the event was observed before last follow-up.

tpos_ind

n*1 vector of whether the event was observed after follow-up started (t>0).

gMat

n*q genotype matrix.

null_beta

(p+nknots+2)*1 vector of coefficients for null model.

Itt

(p+nknots+2)*(p+nknots+2) Fisher information matrix for null model coefficients.

pvalue

Boolean, if TRUE then find the p-value (maybe don't need it if bootstrapping, saves eigendecomposition)

Value

A list with the elements:

p_SKAT

ICSKAT p-value

p_burden

IC burden test p-value

complex

Indicator of whether the SKAT variance matrix was positive definite

sig_mat

The covariance matrix of the score equations for genetic effects when treated as fixed effects

skatQ

SKAT test statistic

burdenQ

Burden test statistic

Ugamma

Score vector

lambdaQ

Vector of eigenvalues of variance matrix

null_beta

The fitted null parameters

err

Will be 0 for no error, 22 if had to adjust parameters on CompQuadForm (totally normal), or 99 if NA in variance matrix. ICSKATwrapper will return 1 here if the null fit has an error

errMsg

Explains error code, blank string if no error

Examples

set.seed(2)
gMat <- matrix(data=rbinom(n=2000, size=2, prob=0.3), nrow=100)
xMat <- matrix(data=rnorm(200), nrow=100)
bhFunInv <- function(x) {x}
obsTimes <- 1:5
etaVec <- rep(0, 100)
outcomeDat <- gen_IC_data(bhFunInv = bhFunInv, obsTimes = obsTimes, windowHalf = 0.1,
probMiss = 0.1, etaVec = etaVec)
lt <- outcomeDat$leftTimes
rt <- outcomeDat$rightTimes
tpos_ind <- as.numeric(lt > 0)
obs_ind <- as.numeric(rt != Inf)
dmats <- make_IC_dmat(xMat, lt, rt, obs_ind, tpos_ind)
nullFit <- ICSKAT_fit_null(init_beta = rep(0, 5), left_dmat = dmats$left_dmat,
right_dmat=dmats$right_dmat, obs_ind = obs_ind, tpos_ind = tpos_ind,
lt = lt, rt = rt)
ICskat(left_dmat = dmats$left_dmat, right_dmat=dmats$right_dmat,
lt = lt, rt = rt, obs_ind = obs_ind, tpos_ind = tpos_ind, gMat = gMat,
null_beta = nullFit$beta_fit, Itt = nullFit$Itt)