small_pre_allocated_windows_processed: List of consecutive SNP windows (filtered and imputed) with...

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

List of consecutive SNP windows (filtered and imputed) with positon labels

Description

Similarly to small_pre_allocated_windows, this dataset contains a list of SNP windows, each formatted as described in documentation for sample_SNP_window. All of these SNP windows are consecutive and span the range of 14.49Mb 14.52Mb on Chr. 10. Each SNP window spans a range of 3kb and consecutive windows are shifted by 1kb relative to the previous adjacent window.

Usage

small_pre_allocated_windows_processed

Format

A list with 90 values

Details

Unlike small_pre_allocated_windows, this object HAS undergone processing to filter out SNPs with high missing rates (> 0.15) or to impute missing values to the mean. Thus, the use of this object will NOT produce warning messages from 'SKAT', as there is no need for ad-hoc missing rate filtering and imputation to be performed.

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