NEWS

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BioQC 1.13.1

• Functions to manipulate GmtList objects are considerably expanded
• All documents and namespaces are now managed by roxygen2
• readGmt by default read unique genes from GMT files

BioQC 1.1-5

• Add C-level implementation of Wilcoxon-Mann-Whitney rank sum test
• Documentation and vignettes updated to be ready for Bioconductor submission.

BioQC 1.1-0

• Dependencies on BIOS has been resolved by copying the C functions into the package, in order to prepare BioQC for public release. It can now be installed on systems where BIOS is not available.
• Clean-ups and updates of documentations.

BioQC 1.0-14

• Add a series of functions related to Shannon entropy: entropy, entropyDiversity, entropySpecificity, sampleSpecialization

BioQC 1.0-13

• Add gini, a function to calculate Gini index. It implements the gini_stat function in the BIOS library

BioQC 1.0-12

• If the p-value is lower than than the threshold of R (about 10E-320) and thus produces a score of -Inf, the value of 320 is used to avoid -Inf as output.

BioQC 1.0-11

• bioqc.Rscript: add command-line option '-appendGmtDesc' to append DESC column in the GMT file to outputs.

BioQC 1.0-10

• bioqc.Rscript: add details in the help information of 'chiptype' option
• bioqc.Rscript: accepts 'GeneID' and 'GeneSymbol' as chiptype in a case-insensitive manner
• Update the gmt file to include a few rat tissues (upstream change by Laura Badi, Sep. 3, 2012)

BioQC 1.0-9

• bioqc.Rscript: the threshold input is first transformed by 10^(-threshold) to make inputting threshold easier

BioQC 1.0-8

• filterPmat fixes the warning message when threshold is NULL: it is tested before is.na

BioQC 1.0-7

• bioqc.Rscript rounds output to two digits

BioQC 1.0-6

• Add absLog10p function to take the absolute base-10 logarithm of p-values
• Add filterPmat

BioQC 1.0-5

• bioqc.Rscript accepts -gmt correctly (before it is -gmtfile)

BioQC 1.0-4

• exp.tissuemark.affy.roche.symbols.gmt were updated by L. Badi, removing suspected contaminated samples
• bioqc.Rscript maps genes to human orthologues from ChipFetcher-exported files

BioQC 1.0-3

• bioqc.Rscript: the dependence on ribiosAnnotation has been simplified: only when chiptype is GeneSymbol, the script does not need ribiosAnnotation
• bioqc.Rscript: annotate GeneID and Probesets have been simplified by using syntax from ribiosAnnotation >= 2.0-0
• bioqc.Rscript: Program exists when no valid GeneSymbol could be found.

BioQC 1.0-2

• bioqc.Rscript: Fix supported.ct2 bug seen on the UDIS machine
• bioqc.Rscript: ribiosIO minimum version 1.0-12 added

BioQC 1.0-1

• wmw.test has been made more robust: in case no TRUE exists in sub, the function does not fail and return 0 (statistic) or 1 (p-value)
• bioqc.Rscript has been added and published under /SOFT/bi/apps/ribios/scripts

BioQC 1.0-0

• Establish the BioQC package
• Add methods wmwTest for Wilcoxon-Mann-Whitney test for several data structures used by BIO-QC procedures
• wmwTest was (almost) fully documented

BioQC 0.99.4

• wmw_test (C function) is refactored

BioQC 0.99-1

• read_gmt checks whether a GMT line is valid; if not, it prints warning message to the error console and skips the line.
• Add following alternatives to wmwTest in order to make the downstream analysis easier: abs.log10.greater, log10.less, abs.log10.two.sided, and Q.
• Two.sided tests return correct value if the gene set is of length 0

BioQC 0.99-0

• Reset the version to 0.99-0 for submission