shinyMethyl

shinyMethyl performs quality control and visualization of DNA methylation data from Illumina 450k arrays to assess data integrity and support methylation analyses such as epigenome-wide association studies (EWAS) and cancer epigenomics.

Key Features:

• QC summarization and export: Summarizes Illumina 450k experiments into compact, exportable R objects that store QC metrics.
• Reactive visualizations and plots: Generates reactive visualizations and plots for sample-level assessment, enabling detection of batch effects and outliers.
• Phenotypic association analysis: Supports exploration of phenotypic associations using coloring techniques and principal component analysis (PCA) to investigate correlations between methylation patterns and phenotypic traits.
• Large-scale dataset handling: Handles extensive datasets typical of EWAS and The Cancer Genome Atlas (TCGA) collections for QC and visualization of Illumina 450k data.
• Bioconductor integration: Produces objects and outputs compatible with Bioconductor and R-based genomic analysis packages.

Scientific Applications:

• Epigenome-Wide Association Studies (EWAS): Facilitates identification and assessment of methylation markers associated with traits or diseases through QC, visualization, and PCA on Illumina 450k data.
• Cancer Genomics: Enables QC and visualization of tumor methylation data from studies such as TCGA to support exploration of epigenetic alterations and biomarker identification.

Methodology:

Implemented in R and leveraging the Bioconductor framework, shinyMethyl summarizes Illumina 450k experiments into exportable R objects and provides reactive visualizations and PCA-based analyses.