NEWS.md

In umr1283/dmapaq: DNA Methylation Arrays Processing And Quality-Control

dmapaq (development version)

• In DESCRIPTION,
  • Add Illumina annotation in GRCh38.
• In rmarkdown templates,
  • Tweak code syntax.
  • Add Illumina annotation in GRCh38.
  • Fix cell composition estimate for CordBloodCombined.
• In read_idats.R,
  • Fix .doSnowGlobals errors within targets.
  • Add Illumina annotation in GRCh38 as default.

dmapaq 0.3.5

• In DESCRIPTION,
  • Remove doParallel.
• In rmarkdown templates,
  • Make sure Sample_ID is a unique string and in the first column of the sample sheet.
  • Remove doParallel.
  • Order PCA association tile plot according to p-values.
• In read_idats.R,
  • Rewrite the build process of the RGChannelSetExtended object.

dmapaq 0.3.4

• In rmarkdown templates,
  • Explicit use of Sample_ID as the unique IDs for samples.
• In read_idats.R,
  • Explicit use of Sample_ID as the unique IDs for samples.

dmapaq 0.3.3

• In rmarkdown templates,
  • Update obsolete captions.
  • Perform independent association testing between technical variables and principal components.
  • Fix ggplot2 issue with legend components defined in theme_set().

dmapaq 0.3.2

• In rmarkdown templates,
  • Remove unnecessary lower condition for outliers.
  • Replace underscore with dash.
  • Fix PCA section.

dmapaq 0.3.1

• In rmarkdown templates,
  • Fix reference for ComBat.
  • Fix missing params in YAML.
• In read_idats.R,
  • Fix dataset for population specific CpG/SNPs.
  • Fix missing params in YAML.

dmapaq 0.3.0

• In rmarkdown templates,
  • Reorder code in setup chunk.
  • Rewrite code using data.table.
• In ggheatmap.R,
  • Remove function ggheatmap().
• In read_idats.R,
  • Optimise code.
  • Use parallel.
  • Use data.table.
  • Add echo parameter.
  • Return log messages.

dmapaq 0.2.0

Minor improvements and fixes

• In DESCRIPTION,
  • Update all packages listed in Imports.
  • Now imports ggplot2 v3.3.0.
  • Use gt for tables.
• In README.Rmd, remove parallel function for ComBat batch correction.
• In rmarkdown template,
  • Fix regular expression for reference panel.
  • Fix library availability check for cordbloodcombined reference panel.
  • Fix misplaced parenthesis around calls to system.file().
  • Fix missing probe id in beta matrix output.
  • Fix missing prefix.
  • Fix cell composition section when no tissue is provided.
  • Fix gender discrepancy table when observed gender is missing.
  • Fix call rates table not displaying all thresholds.
  • Remove parallel computation for ComBat batch correction.
  • Replace requireNamespace() with system.file() in order to check packages availability.
  • No longer show empty gender check table.
• In R/qc_idats.R.
  • Import gt for tables.
  • Remove import for kableExtra.
• Remove R/ComBat.mc.

dmapaq 0.1.0

New features

• read_idats() allows to efficiently import idats files mostly using minfi functions.
• qc_idats() allows to compute quality-control of methylation array from Illumina using a rmarkdown template.
• ggheatmap() allows to compute heatmap with dendrogram on x-axis and y-axis using ggplot2.
• ComBat.mc() is a multi-processor wrapper for ComBat method (initially in ENmix).

umr1283/dmapaq documentation built on Dec. 23, 2021, 2 p.m.