Changes in version 1.13.14 (2020-03-03) Changes in existing functions o inherits(a, b) is now used instead of class(a)==b. Changes in version 1.13.6 (2020-01-03) Changes in existing functions o doSave was added to the combine.networks() function. Changes in version 1.13.4 (2019-11-19) Bug Fixes o In the combine.networks() function, the netwok typo was fixed. Changes in version 1.11.34 (2019-10-21) General o The pipeline is now explained step by step in the vignette. Changes in version 1.11.32 (2019-10-18) Changes in existing functions o The Data argument of compute.pigengene can now be a matrix with only 1 column. Changes in version 1.11.30 (2019-10-02) Changes in existing functions o The doRetuNetworks argument is now added to the combine.networks function. Changes in version 1.11.28 (2019-10-01) New functions o message.if() is now exported. Changes in version 1.11.26 (2019-09-26) Changes in existing functions o Better QC in the gene.mapping() function, the possible keys will be printed if the input is not appropriate. New functions o save.if() is now exported. Changes in version 1.11.24 (2019-09-03) Bug Fixes o In the combine.networks() function, selectedModules does not need to be "All". Also, if saveFile=NULL, nothing will be saved without any error. Changes in version 1.11.20 (2019-05-15) Changes in existing functions o Data and Labels can now be lists, which will be combined using combine.networks() before analysis. Changes in version 1.11.4 (2019-05-02) Bug Fixes o repeat.data(times=1,...) now produces valid output. Changes in version 1.9.26 (2019-04-24) Bug Fixes o In the compute.pigengene function, if a module has only one gene, its name is now not omitted in the csv file. Changes in version 1.9.24 (2019-04-24) Changes in existing functions o An object of pigengene-class can now have a heavyToLow attribute. Changes in version 1.9.20 (2019-04-12) Changes in existing functions o In the compute.pigengene function, the columns of Data and names of modules can now differ. Changes in version 1.9.14 (2019-02-12) Changes in existing functions o The dOrderByW argument is now added for the compute.pigengene function. Changes in version 1.9.8 (2018-11-22) Changes in existing functions o All of the learn.bn function can now be set from one.step.pigengene through bnArgs. Changes in version 1.9.4 (2018-11-16) Changes in existing functions o gene.mapping can now output multiple conventions. Changes in version 1.7.2 (2018-05-22) General o The version of the package C50 is now required to be at least 0.1.2, which exports the as.party.C5.0() function. Changes in version 1.5.22 (2018-04-28) Bug Fixes o stats::cor is used in compute.pigengene and draw.cor functions. See the NAMESPACE for the important reason. Changes in version 1.5.9 (2018-03-12) General o cor is imported from WGCNA, but not from stats, because WGCNA does not call the cor function properly. Changes in existing functions o RsquaredCut is added to the arguments of the one.step.pigengene function. Changes in version 1.5.6 (2018-01-19) Changes in existing functions o In the get.fitted.leaf function, the function C50:::as.party.C5.0 is used, which used to be exported in the previous versions of C50, but not in version 0.1.1. Changes in version 1.5.2 (2017-11-10) New functions o The check.nas function is now exported. Changes in version 1.3.8 (2017-09-13) Changes in existing functions o Order of conditions in pheatmap.type can now be determined by the user. Changes in version 1.3.6 (2017-08-20) Changes in existing functions o A bug in gene.mapping () function fixed to better map probe IDs. Changes in version 1.3.4 (2017-07-31) Changes in existing functions o The doTranspose argument added to the heatmap.type() function. Changes in version 1.1.14 (2017-05-10) Changes in existing functions o A bug in the module.heatmap() function fixed. Changes in version 1.1.12 (2017-04-15) Changes in existing functions o The mouseHomologFilter argument is added to the unexported furntion hu.mouse() with a default value of "with_mmusculus_homolog". This is now compatible with biomaRt_2.30.0, it used to be "with_homolog_mmus" in older versions of biomaRt. Changes in version 1.1.10 (2017-03-30) Changes in existing functions o Checking the pigengene input of module.heatmap(). o Issues in the balance() function (not exported) where Labels is a factor are resolved. Also, if all sampls have the same size, oversampling is automatically turned off. o If Labels is a factor, it is now converted to a character vector in check. pigengene.input(). Changes in version 1.1.6 (2017-03-27) Changes in existing functions o The module.heatmap() function now has the doAddEigengene and scalePngs arguments. o The compute.pigengene() function now reports also the size of modules in the pigengene_pvalue.csv output file. Changes in version 0.99.25 (2016-10-02) Changes in existing functions o The compute.pigengene() function now uses welch.pvalue() instead of pvalues.manov(). Changes in version 0.99.8 (2016-05-18) General o Under review by Bioconductor. o Created.