pleio_test {pleiotest}

Sequential Wald test for pleiotropy

Description

Performs the sequential test of pleiotropic effects using results of pleioR().

Usage

pleio_test(
  pleio_results,
  loop_breaker = 1,
  save_at = NULL,
  contrast_matrices_list = NULL
)

Arguments

pleio_results

pleio_class object returned by pleioR().

loop_breaker

numeric value for a maximum p-value used to stop the sequence if a higher p-value is obtained. This saves computation time if there are many tests to perform.

save_at

character with directory and/or file name (.rdata) to save the results. This is useful when handling multiple results such as in parallel jobs.

contrast_matrices_list

user-specified contrast matrices within a list of lists, or a single contrast matrix (see example). Each matrix must have the same number of columns, and must be equal to the number of traits.

Value

list of p-values, indices, and trait numeric identifier.

Examples

# Example of user-specified contrast matrices with 3 traits
cm1 <- matrix(c(-1, 0, 1), ncol = 3)
cm2 <- matrix(c(0, -1, 1), ncol = 3)
contrast_matrices <- list('1vs3' = list(cm1), '2vs3' = list(cm2))
# or a single contrast matrix as:
contrast_matrices <- cm1