re_allocate_windows: Obtain a new list of SNP windows, based on p-values from an...

In naglemi/mtmcskat: Multi-Threaded Monte Carlo Sequence Kernel Association Test (MTMC-SKAT)

Obtain a new list of SNP windows, based on p-values from an earlier list

Description

Obtain a new list of SNP windows, based on p-values from an earlier list

Usage

re_allocate_windows(
  x,
  upper_bound,
  lower_bound,
  pre_allocated_SNP_windows,
  top_N = Inf
)

Arguments

x	An output from mtskat or a similarly formatted x.frame
upper_bound	A numeric value corresponding to the maximum p-value for the range of interest
lower_bound	A numeric value correspondign to the minimum p-value for the range of interest
pre_allocated_SNP_windows	Output from pre_allocate, which is a list of lists, with each sub-list containing elements as described in documentation for extract_window
top_N	Integer representing the number of top associations on which the user wishes to perform resampling. For example, if this value is set to 5, any SNPs that do not produce p-values among the lowest 5 will not be included in outputs from this function.

Value

Output is the same format as for pre_allocate: a list of lists, with each sub-list containing elements as described in documentation for extract_window

Examples

data("small_pre_allocated_windows")
data("small_mtskat_results")

re_allocate_windows(
  x = small_mtskat_results,
  upper_bound = 0.01,
  lower_bound = 0.001,
  pre_allocated_SNP_windows = small_pre_allocated_windows)

naglemi/mtmcskat documentation built on Aug. 23, 2023, 5:35 p.m.