lm_qvalue {swfdr} | R Documentation |
The recipe for turning pvalues into qvalues is adapted from package 'qvalue' and articles by Storey, Tibshirani, Taylor, Siegmund.
lm_qvalue( p, X, pfdr = FALSE, pi0 = NULL, smoothing = c("unit.spline", "smooth.spline"), ... )
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. If this is not provided, pi0 is estimated using function 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) |
object of class ‘lm_qvalue’, which is a list with several components
call |
matched function call |
pvalues |
numeric vector of original p-values |
qvalues |
numeric vector of q-values |
|
other list elements transferred from pi0 |
# define a covariate X <- rep(c(0, 1), each=1000) # generate p-values, randomly for group 0 and with low values for group 1 pVal <- c(runif(1000), rbeta(1000, 0.2, 1)) # compute qvalues, using the covariate qVal <- lm_qvalue(pVal, X=X)