sample_SNP_window_processed: Labeled window of alt. allele counts (filtered and imputed)...

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

Labeled window of alt. allele counts (filtered and imputed) for P trichocarpa

Description

A dataset containing the position of a SNP window in the genome and all of the alternative allele counts for each SNP within the SNP window

Usage

sample_SNP_window_processed

Format

A list containing three values

Position

Integer, the position of the center of a SNP window, in base pairs

Z

Matrix of integers containing alternative allele counts for each of 175 SNPs (columns) in the SNP window, across 200 genotypes (rows)

Chr

Integer or character indicating the chromosome or other scaffold, respectively, on which the SNP window is found

Details

Unlike sample_SNP_window, 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.

Support for the Poplar GWAS dataset is provided by the U.S. Department of Energy, Office of Science Biological and Environmental Research (BER) via the Bioenergy Science Center (BESC) under Contract No. DE-PS02-06ER64304. The Poplar GWAS Project used resources of the Oak Ridge Leadership Computing Facility and the Compute and Data Environment for Science at Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725

Source

https://cbi.ornl.gov/data

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