NEWS

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MLP 1.43.1

• getGeneSets: add 'Rhesus' to 'species' (available only for 'GOBP', 'GOMF', 'GOCC' or 'KEGG')

MLP 1.39.1

• use Imports rather than Depends
• use Authors@R
• KEGG.db (not available from BioC >= 3.13) -> KEGGREST
• getGeneSets: only return descriptions for selected pathways
• update example gene set

MLP 1.21.1

• mlpBarplot: add ylab, cex, use title instead of mtext to set title
• plotGOgraph: add nCutDescPath, replace '\\\n' by \n', add error when graphs without edges

MLP 1.5.2

• remove require(mouse4302mmentrezg.db) calls to keep R CMD check from giving inappropriate warnings

MLP 1.5.0

• update exampleGeneSet.rda using GO.db for BioC 2.11

MLP 1.4.2

• further improvements in getGeneSets and addGeneSetDescription

MLP 1.4.1

• better checks on geneSetSource in getGeneSets

MLP 1.3.0

• update using new annotation packages
• move to roxygen2

MLP 1.2.1

• also export addGeneSetDescription

MLP 1.2.0

• BioC release 2.9

MLP 1.1.1

• update using new annotation packages
• apply changes to column permutations (contributed by Heather Turner)

MLP 0.99.5

• further adaptations for use with the reactome.db package

MLP 0.99.4

• adapt MLP for use with the reactome.db package (Willem Ligtenberg)

MLP 0.99.3

• fix mlpBarplot (p values equal to 0) reported and patched by Willem Ligtenberg

MLP 0.99.2

• fix bug in plotGeneSetSignificance (barColors argument)

MLP 0.99.1

• fix mouse4302.db dependency of vignette

MLP 0.99.0

• no longer export utility functions

MLP 0.0-14

• add examples to help pages

MLP 0.0-13

• comply with R 2.12.x

MLP 0.0-12

• fix main title handling in plotGOgraph
• fix main title handling for mlpBarplot in case the geneSetSource are external data (data frame)

MLP 0.0-11

• fix in plotGeneSetSignificance (psids)
• typo NEWS file

MLP 0.0-10

• updated vignette
• change argument criticalValues of the MLP function to probabilityVector
• trivial change example data set

MLP 0.0-9

• updated default grey scales for plot(., type = "barplot")
• default grey for plotGeneSetSignificance set to 'grey50'
• substantial improvement to vignette (An)
• uniform use of 'main' argument for main titles in plot functions

MLP 0.0-8

• add Dog species funcionality to getGeneSets (public GO and KEGG annotation only)
• getGeneSets: replace eset argument by entrezIdentifiers argument
• use geneSetSource instead of pathwaySource for uniformity across all functions (most notably getGeneSets)
• plot(., type = "barplot") now allows for specifying colors for the bars (barColors argument) and includes fix
• fix colors and legend for plot(., type = "GOgraph")
• added plotGeneSetSignificance
• impose character type for geneSetDescription in MLP output (instead of factor)

MLP 0.0-7

• add type = "GOgraph" to the plot method for MLP objects
• rudimentary draft for vignette included

MLP 0.0-6

• store pathwaySource information in MLP output object
• integrate addGeneSetDescription into MLP function and adapt mlpBarplot accordingly
• remove plot argument from quantileCurves (argument was not used)
• introduce plot method with support for type = "barplot" and type = "quantileCurves"

MLP 0.0-5

• goAnnotation replaced by the more general getGeneSets (for other pathway sources than the GO data base)
• added mlpBarplot

MLP 0.0-4

• significant speedups for goAnnotation and addGeneSetDescription
• renamed summary.MLP to addGeneSetDescription
• add support for dogs
• documentation fixes
• remove (deprecated) goInputMLP
• remove dead code in goAnnotation
• remove pperm, tStatistic and their utility functions (limma being preferred)

MLP 0.0-3

• fix probeset names (exclude non-numeric ones)

MLP 0.0-2

• fix in summary.MLP

MLP 0.0-1

• first package version