Calculate q-values — calc_qvalue • helpr

Calculates a vector of q-values corresponding to a vector of p-values.

Usage

calc_qvalue(
  p,
  lambda = seq(0, 0.95, 0.01),
  lambda_eval = NULL,
  match_storey = FALSE
)

# S3 method for class 'q_value'
plot(x, ..., rng = c(0, 0.25))

Arguments

p: A vector of p-values.
lambda: A sequence of lambdas to evaluate.
lambda_eval: A value of lambda to evaluate at, defaults to the maximum value of the lambda sequence.
match_storey: logical(1). Should the output be matched to Storey's qvalue() function?
x: A q_value class object.
...: Additional arguments passed to the S3 plot generic.
rng: numeric(2). Range of values.

Value

A list of class q_value containing:

call: The original call to calc_qvalue().
p_value: The original vector of p-values.
m: ?
lambda: ?
lambda_eval: ?
pi_lambda: ?
spline_fit: ?
pi0: ?
q_value: A a vector of q-values.

A cool plot.

References

John Storey. PNAS. 2003.

See also

smooth.spline()

Author

Stu Field

Examples

x <- withr::with_seed(101, c(seq(0.0001, 0.05, length = 50), runif(950)))
q <- calc_qvalue(x)

# S3 plot method
plot(q)