donkang75/MetaQC: MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis

MetaQC implements our proposed quantitative quality control measures: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). (See the reference for detailed explanation.) For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion/exclusion decision.

Getting started

Package details

AuthorDon Kang <[email protected]> and George Tseng <[email protected]>
MaintainerDon Kang <[email protected]>
LicenseGPL-2
Version0.1.14
URL https://github.com/donkang75/MetaQC
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("donkang75/MetaQC")
donkang75/MetaQC documentation built on May 15, 2019, 10:41 a.m.