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Changes in ribiosExpression

Changes in version 1.3.5

Bioconductor preparation

  • Added biocViews to DESCRIPTION.
  • Added BiocStyle vignette.
  • Updated R dependency to >= 4.4.0.
  • Added @return tags to all exported functions.
  • Fixed typos in documentation.
  • Replaced class(x) %in% with is.numeric().
  • Converted NEWS to NEWS.md format.

Changes in version 1.0-39

  • parseDesignContrast adds new parameter expSampleNames to allow sample name consistency check with input matrix.

Changes in version 1.0-34

  • DesignContrast prints error message if validity is violated.
  • parseDesignContrastFile fixes a mistake of assigning group levels.
  • parseDesignContrastFile now accepts the dispLevelStr option.

Changes in version 1.0-33

  • parseDesignContrastStr fixes two errors.

Changes in version 1.0-32

  • Add DesignContrast object.

Changes in version 1.0-29

  • Add new functionality in keepMaxMeanProbes.Rscript: able to read from .CHIP file.
  • keepMaxMeanProbes.Rscript now does not depend on the S4 class ExpressionSet anymore, therefore much faster.

Changes in version 1.0-28

  • Debug keepMaxMeanProbes.Rscript: extname returns NA if not found, therefore an additional check is added.

Changes in version 1.0-27

  • Function extension in ChipFetcher2ExpressionSet: now non-Affymetrix probesets are supported as well.

Changes in version 1.0-26

  • The main body of readCls has been moved to ribiosIO::read_cls. readCls becomes a synonym for compatibility.

Changes in version 1.0-25

  • Improvement in readCls: error messages provide more informative details for mal-formatted files.

Changes in version 1.0-24

  • Bug fix in writeEset: expression matrix is written without quotes.
  • New script: keepMaxMeanProbes.Rscript filters duplicated genes by taking the one with maximum average expression.

Changes in version 1.0-23

  • Bug fix in readGct: if input feature names have duplicates, the exprs matrix row names are changed.

Changes in version 1.0-22

  • Move exprsMat2gct.Rscript to the ribiosIO package.
  • writeGct has been refactored for matrix in ribiosIO, and re-implemented as an S4-method for matrix and ExpressionSet.

Changes in version 1.0-21

  • Add exprsMat2gct.Rscript to convert between expression matrix files and GCT files.

Changes in version 1.0-20

  • ChipFetcher2ExpressionSet: add option orthologue.
  • keepMaxStatProbe uses function(x) mean(x, na.rm=TRUE) as default function.

Changes in version 1.0-19

  • limma2gsea.Rscript is updated.

Changes in version 1.0-18

  • Refactor GSEA-related functions that are not dependent on the Biobase data structure to the ribiosGSEA package.

Changes in version 1.0-17

  • limma2gsea.Rscript guarantees no replicated gene symbols after orthologue mapping.

Changes in version 1.0-16

  • Add limma2gsea.Rscript to inst/Rscript.

Changes in version 1.0-15

  • The ribiosAnnotation package has been removed from the dependency list.
  • Add comp_diff.Rscript to inst/Rscript.

Changes in version 1.0-14

  • The deprecation message of remainHighestVarProbe and keepHighestVarProbe have been updated.

Changes in version 1.0-13

  • The rowscale method warns if the input ExpressionSet does not have 'lockedEnvironment' as storageMode.

Changes in version 1.0-12

  • Low-level functions for computational drug repositioning refactored into ribiosReposition.

Changes in version 1.0-11

  • Add feature in summarizeProbesets: option keep.featureNames.
  • Rename and rewrite sprintGmt to formatGmt as S4 method.

Changes in version 1.0-10

  • Bugfix in readEset for numeric column names.
  • Add annotate and reannotate methods.
  • Add documentation for the ribios.ExpressionSet object.

Changes in version 1.0-9

  • Add kendallW function and kendallWmat S4-method.

Changes in version 1.0-8

  • PCA-related data structures and functions are refactored into the ribiosPCA package.

Changes in version 1.0-7

  • Add summarizeProbesets to summarize probesets.
  • NAMESPACE are now explicitly stated.

Changes in version 1.0-6

  • Add dependency on the ribiosAnnotation package.
  • Add writeEset and readEset functions.
  • readFKdata was renamed as readFKtable.

Changes in version 1.0-5

  • Add git version control.

Changes in version 1.0-4

  • Move data.frame and matrix functions to the ribiosUtils package.

Changes in version 1.0-3

  • Refactor read_gct into ribiosIO for efficiency.

Changes in version 1.0-2

  • Change keepHighestVarProbe to more generalized keepMaxStatProbe.

Changes in version 1.0-1

  • Remove the path option from the readGctCls function.