parameters_in_locfdr: parameters_in_locfdr

In annahutch/fcfdr: Flexible cFDR

Description

parameters_in_locfdr

Usage

parameters_in_locfdr(
  p,
  q,
  indep_index,
  res_p = 300,
  res_q = 500,
  maf = NULL,
  check_indep_cor = TRUE,
  enforce_p_q_cor = TRUE
)

Arguments

p	p values for principal trait (vector of length n)
q	continuous auxiliary data values (vector of length n)
indep_index	indices of independent SNPs
res_p	resolution for p
res_q	resolution for q
maf	minor allele frequencies for SNPs to which p and q relate (optional and used to perform MAF matching)
check_indep_cor	check that sign of the correlation between p and q is the same in the independent subset as in the whole
enforce_p_q_cor	if p and q are negatively correlated, flip the sign on q values

Value

list of values used as input into locfdr::locfdr function intrinsically in flexible_cfdr

Examples

# In this example, we generate some p-values (representing GWAS p-values)
# and some arbitrary auxiliary data values (e.g. representing functional genomic data).
# We use the parameters_in_locfdr() function to extract the parameters estimated by
# the locfdr function.

# generate p
set.seed(1)
n <- 1000
n1p <- 50 
zp <- c(rnorm(n1p, sd=5), rnorm(n-n1p, sd=1))
p <- 2*pnorm(-abs(zp))

# generate q
mixture_comp1 <- function(x) rnorm(x, mean = -0.5, sd = 0.5)
mixture_comp2 <- function(x) rnorm(x, mean = 2, sd = 1)
q <- c(mixture_comp1(n1p), mixture_comp2(n-n1p))

n_indep <- n

parameters_in_locfdr(p, q, indep_index = 1:n_indep)

annahutch/fcfdr documentation built on Feb. 12, 2022, 6:49 a.m.