lm_qvalue {swfdr}R Documentation

Compute qvalues taking into account a matrix of covariates

Description

The recipe for turning pvalues into qvalues is adapted from package 'qvalue' and articles by Storey, Tibshirani, Taylor, Siegmund.

Usage

lm_qvalue(p, X, pfdr = FALSE, pi0 = NULL,
  smoothing = c("unit.spline", "smooth.spline"), ...)

Arguments

p

numeric vector of p-values

X

matrix of covariates (can be missing if pi0 is specified instead)

pfdr

logical, making estimates robust for small p-values and a small sample size

pi0

list with pi0 estimates from lm_pi0

smoothing

character, type of smoothing used to fit pi0. Note the default in this function is different than in lm_pi0.

...

other parameters (passed on to lm_pi0 if pi0 is not provided)

Value

list


[Package swfdr version 1.12.0 Index]