Package: recountmethylation 1.23.0

Probe manifest background | Getting the HM450K manifest annotations from an RGChannelSet | Getting the EPIC manifest annotations from an RGChannelSet | Annotation-based probe filters | Filtering on common SNPs | Filtering on cross-reactive CpG probes | Querying and quantifying genome regions and functional groups | Find probes mapping to a gene | Viewing gene functional region frequencies | Identifying promoter-mapping and gene body-mapping CpG probes | CG Island annotations | Conclusions

Overview | Analysis script and limited chunk evaluation | Datasets and data objects | Example 1: Comparing mined and predicted age | Make new variables and filter samples | Analyses and summary statistics | Scatter plots of study errors and sample ages | Example 2: Signal comparison of FFPE and frozen samples | Get samples with storage type information | Use blocking to calculate signal log2 medians | Signals plotted by storage type | Example 3: Identify and analyze tissue-specific probes with the highest | Sample identification and summary | Calculate log2 methylated and unmethylated signal medians | Perform linear correction on DNAm for study IDs | Perform array-wide ANOVAs and filter probes | Get probe DNAm summary statistics and analyze variances | Violin plots and heatmaps of probe set DNAm means and variances | Conclusions | Session info | Works Cited

Background: search indexes for biological data | Index samples on dimension-reduced data | Virtual environment setup | Perform dimensionality reduction on DNAm data | Make a new HNSW search index | Query nearest neighbors in the search index | Get nearest neighbors from search index queries | Inspect query results | Plot metadata labels among nearest neighbors | Metadata label frequency among neighbors from a single query | Distribution of neighbors labeled whole blood across queries | Distributions of multiple labels and queries | Session Info | Works Cited

Obtaining example data | Converting data | Converting data between platforms | Converting data between SummarizedExperiment classes | Converting between standard and DelayedArray-backed objects | Choosing the correct data type to use | Saving data | Saving flat tables from DNAm array datasets | Saving SummarizedExperiment objects | Saving DelayedArray-backed objects | Conclusions

Introduction and overview | Compilation releases | Database files and access | ExperimentHub integration | Disclaimer | Background | DNAm arrays | SummarizedExperiment object classes | Database file types | Sample metadata | HDF5-SummarizedExperiment example | Obtain the test database | Inspect and summarize the database | HDF5 database and example | Validate DNAm datasets | Download and read IDATs from the GEO database server | Compare DNAm signals | Compare DNAm Beta-values | Troubleshooting and tips | Issue: large file downloads don't complete | Issue: unexpected function behaviors for DelayedArray inputs | Get more help | Session info | Works Cited

Obtain the GLINT software | Virtual environment setup | Process example DNAm array data | Further reading | Session Info | Works Cited

Source the revised function, pwrEWAS_itable() | Generate DNAm summary statistics | Run pwrEWAS_itable() | Run power simulations with 2 cores | Access the power analysis results | Plot smooths with errors using ggplot2 | Next steps and further reading | Session Info | Works Cited