Adds QC functions for BeadArray metrics and log M/U signals
Adds data and accessor function for cross-reactive CpGs
Adds vignette showing how to do power analysis with pwrEWAS
Adds vignette showing how to infer genetic ancestry using GLINT/EPISTRUCTURE
Adds vignette showing how to do nearest neighbors search using a search index
Adds functions for feature hashing, search index construction, and KNN search
Improves User's Guide, fixes typos, new citation, adds disclaimer text, updates servermatrix() chunk.
Updates examples to further limit downloads. Function get_rmdl() uses download = FALSE,
Updates Data Analyses vignette. Uses reduced dpi for images in Data Analyses vignette to limit package size. Uses updated metadata file name.
Compresses new metadata v.0.0.2 files to limit package size.
Uses uniform metadata file label for v.0.0.1 file.
Added v.0.0.2 database compilation files to server (recount.bio/data) and revised recountmethylation functions for cross-platform support. The new files reflect IDAT downloads completed in Nov 2020 from GEO/GDS, including the first compilations of EPIC/HM850K arrays.
Added 'platform' argument in relevant 'getdb' functions.
Added 'which.platform' argument to 'get_rmdl'
Added new function 'smfilt' to filter server data table for newest compilation files, accounting for platform in the filename.
Cleaned up and shoretened the 'servermatrix' function. This now handles RCurl call for "dn" (originally from 'get_rmdl') when handling condition 'dn = NULL'.
Updated the User's Guide to fix typos, reflect v.0.0.2 samples, and add a download troubleshoot section. Added numeric citations format, removed evaluation of validation section due to possible package build failure from bad internet connection.
Updated ExperimentHub file metadata script and table to add new v.0.0.2 compilation files.
Renamed sample metadata directory to "gsm_metadata" to avoid confusion with "metadata.csv" file table for hubs.
Added getdb functions for database file download and load
Added servermatrix function to get latest database file metadata
Added User's Guide and Data Analyses vignettes
Added metadata and data_analyses.RData to /inst/extdata
Added key query/accessor functions.
Added package vignette.