Package: MetaSKAT 0.90

Seunggeun (Shawn) Lee

MetaSKAT: Meta Analysis for SNP-Set (Sequence) Kernel Association Test

Functions for Meta-analysis Burden Test, Sequence Kernel Association Test (SKAT) and Optimal SKAT (SKAT-O) by Lee et al. (2013) <doi:10.1016/j.ajhg.2013.05.010>. These methods use summary-level score statistics to carry out gene-based meta-analysis for rare variants.

Authors:Seunggeun Lee [aut, cre]

MetaSKAT_0.90.tar.gz
MetaSKAT_0.90.tar.gz(r-4.5-noble)MetaSKAT_0.90.tar.gz(r-4.4-noble)
MetaSKAT_0.90.tgz(r-4.4-emscripten)MetaSKAT_0.90.tgz(r-4.3-emscripten)
MetaSKAT.pdf |MetaSKAT.html✨
MetaSKAT/json (API)

# Install 'MetaSKAT' in R:
install.packages('MetaSKAT', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.30 score 1 stars 20 scripts 375 downloads 8 exports 7 dependencies

Last updated 2 months agofrom:61cb579bbc. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 08 2024
R-4.5-linux-x86_64OKDec 08 2024

Exports:Generate_Meta_FilesGenerate_Meta_Files_FromDosageMeta_Null_ModelMeta_Null_Model_EmmaXMetaSKAT_MSSD_ALLMetaSKAT_MSSD_OneSetMetaSKAT_wZOpen_MSSD_File_2Read

Dependencies:latticeMatrixRcppRcppEigenRSpectraSKATSPAtest

SKAT

Rendered fromMetaSKAT.Rnwusingutils::Sweaveon Dec 08 2024.

Last update: 2020-11-14
Started: 2013-10-10

Readme and manuals

Help Manual

Help pageTopics
Example datasetExample
Generate summary statistics filesGenerate_Meta_Files Generate_Meta_Files_FromDosage
Get parameters and residuals from H0Meta_Null_Model Meta_Null_Model_EmmaX
Meta analysis SKAT with summary data from each study cohort.MetaSKAT_MSSD_ALL MetaSKAT_MSSD_OneSet
Meta analysis SKAT with individual level genotype dataMetaSKAT_wZ
Read Meta SSD and Info filesOpen_MSSD_File_2Read