Package: regionalpcs 1.3.0

Tiffany Eulalio

regionalpcs: Summarizing Regional Methylation with Regional Principal Components Analysis

Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.

Authors:Tiffany Eulalio [aut, cre]

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regionalpcs.pdf |regionalpcs.html✨
regionalpcs/json (API)
NEWS

# Install 'regionalpcs' in R:

install.packages('regionalpcs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tyeulalio/regionalpcs/issues

On BioConductor:regionalpcs-1.3.0(bioc 3.20)regionalpcs-1.2.0(bioc 3.19)

bioconductor-package

6 exports 0.91 score 80 dependencies

Last updated 2 months agofrom:0129b26a05

Exports:combine_results compute_dimension compute_regional_pcs create_region_map get_sig_pcs summarize_region

Dependencies:abind askpass beachmat BH BiocGenerics BiocParallel BiocSingular cli codetools colorspace cowplot cpp11 crayon curl DelayedArray DelayedMatrixStats dplyr dqrng fansi farver formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel glue gtable httr IRanges irlba isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl PCAtools pillar pkgconfig plyr R6 RColorBrewer Rcpp reshape2 rlang rsvd S4Arrays S4Vectors ScaledMatrix scales sitmo snow SparseArray sparseMatrixStats stringi stringr sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

regionalpcs

Tiffany Eulalio

Rendered fromregionalpcs.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-10-12
Started: 2023-04-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Combine results dataframes across regions	combine_results
Compute significant dimensions of a matrix using the Marchenko-Pastur or Gavish-Donoho methods	compute_dimension
Compute regional principal components for methylation data	compute_regional_pcs
Create a Region Map Between CpGs and Gene Regions	create_region_map
Get significant principal components	get_sig_pcs
Summarize a region using regional principal components	summarize_region