cSeq: Bounding Sequence

In JessieJeng/wsiHD: Weak Signal Inference Under High Dimensionality

Bounding Sequence

Description

Estimates the bounding sequence.

Usage

cSeq(pval_null, ...)

## S4 method for signature 'ANY'
cSeq(pval_null, ...)

## S4 method for signature 'matrix'
cSeq(pval_null, alpha = 0.1)

## S4 method for signature 'big.matrix'
cSeq(pval_null, alpha = 0.1)

## S4 method for signature 'ff_matrix'
cSeq(pval_null, alpha = 0.1)

Arguments

pval_null	A numeric matrix object, a big.matrix object, or an ff_matrix object of dimension p x n. The p-values generated from the null distribution. The columns correspond to the samples (n), the rows to the signals (p).
...	Ignored.
alpha	A numeric object. The significance level. The bounding sequence is estimated as the (1-alpha)-th quantile.

Details

The p-values can be provided as a numeric matrix, a big.matrix as defined by the bigmemory package, or as an ff_matrix as defined by the ff package. The latter two options allow for larger matrices. Please see the documentation of these packages for details on creating objects.

The quantile() function of base R provides 9 algorithms for estimating the quantile, which are based on the definitions of Hyndman and Fan (1996). We have chosen the default (type = 7) here. However, the quantile algorithm implemented in Armadillo is type = 5 and that of ff is type = 1. Thus the results obtained using base, bigmemory, and ff objects containing equivalent data might differ slightly.

Value

An S3 object of class wsiHD comprising a list of length 2.

$c05	is the bounding sequence estimated with delta as the square root of the p-value.
$c1	is that with delta equal to the p-value.

Examples

   data(wsiData)

   set.seed(1234)

   # limit data to expedite example
   smp <- sample(x = 2:4089, size = 500, replace = FALSE)

   Sigma <- stats::cor(x = wsiData[,smp])

   n <- 100L
   p <- ncol(x = Sigma)

   zz <- MASS::mvrnorm(n = n, mu = rep(x = 0.0, times = p), Sigma = Sigma)
   pval_null <- {1.0 - stats::pnorm(q = abs(x = zz))}*2.0

   cSeq(pval_null = pval_null, alpha = 0.1)

JessieJeng/wsiHD documentation built on May 10, 2022, 12:33 a.m.