Changes in version 1.27.16 (2023-06-16)                 

Changes in existing functions

    o   Scaling is done in the compute.pigengene() function to avoid
	the following error that Sogand detailes on her lano: Error in
	La.svd(x, nu, nv) : error code 1 from Lapack routine 'dgesdd'

                 Changes in version 1.27.2 (2023-05-12)                 

Changes in existing functions

    o   The compute.pigengene() function does not warn about almost
	constant genes.

                Changes in version 1.25.16 (2023-03-22)                 

Changes in existing functions

    o   Constant genes are now ignored in the
	compute.pigengene(doWgcna=FALSE,...) function to prevent a run
	time error.

                Changes in version 1.25.12 (2023-03-02)                 

Changes in existing functions

    o   The default value changed in gene.mapping(leaveNA=FALSE, ...).

                Changes in version 1.25.10 (2023-01-04)                 

Changes in existing functions

    o   The doWgcna option is added to the compute.pigengene function.

                 Changes in version 1.25.4 (2022-12-01)                 

Changes in existing functions

    o   The get.enriched.pw function adds gene symbols in the excel
	file.

                 Changes in version 1.23.4 (2022-05-23)                 

Changes in existing functions

    o   The beta table can now be suppressed in the determine.modules
	function.

                Changes in version 1.21.40 (2022-04-15)                 

Changes in existing functions

    o   Habil changed the default value from
	hu.mouse(host="useast.ensembl.org", ...) to
	hu.mouse(host="www.ensembl.org", ...) to prevent a check error
	on Bioconductor.

                Changes in version 1.21.36 (2021-11-16)                 

Changes in existing functions

    o   Habil added the doReturNetworks argument to
	one.step.pigengene().

                Changes in version 1.21.34 (2021-11-12)                 

Changes in existing functions

    o   Habil renamed identify.modules() to determine.modules().

                Changes in version 1.21.30 (2021-11-12)                 

New functions

    o   Neda exported identify.modules(), make.filter(), and
	apply.filter() functions.

                Changes in version 1.19.50 (2021-10-14)                 

New functions

    o   Neda added the identify.modules(), make.filter(), and
	apply.filter() functions, but not exported them yet.

                Changes in version 1.19.30 (2021-09-08)                 

Bug Fixes

    o   The averaged.network() function does not have the nodes
	argument in bnlearn Version >=4.7, and thus this argument was
	removed.

                Changes in version 1.19.24 (2021-08-06)                 

New functions

    o   The get.enriched.pw() function is added.

Bug Fixes

    o   A bug fix in the gene.mapping() function that used to occur
	when we had multiple output databases.

                Changes in version 1.19.10 (2021-06-25)                 

Changes in existing functions

    o   The message.if() function can now write the message in a text
	file.

                 Changes in version 1.19.8 (2021-05-25)                 

Bug Fixes

    o   The C50 plot function seems to have different behavior when the
	number of Labels is 2. Habil reverse the color to fix the
	resulting bug.

                Changes in version 1.17.10 (2021-02-02)                 

Bug Fixes

    o   When building the Ubuntu, Neda got an error message on building
	the vignette "argument is of length zero". It was due to her
	old version of BiocStyle, 2.14.4. To solve this issue,
	Pigengene now depends BiocStyle Version >= 2.19.1. Even 2.18.1
	might be enough with R 4.0.3.

                Changes in version 1.15.20 (2020-09-28)                 

Changes in existing functions

    o   When automatically computing the threshold in the consensus
	function, we now do not allow it to be more than 1 to be
	compatible with bnlearn 4.6.1.

                Changes in version 1.15.16 (2020-09-22)                 

Changes in existing functions

    o   The modules can now be determined in the module.heatmap
	function using the new mes argument.

                Changes in version 1.15.14 (2020-09-08)                 

Bug Fixes

    o   combine.networks now really removes the big TOM file when
	doRemoveTOM=TRUE.

                Changes in version 1.15.12 (2020-06-22)                 

Changes in existing functions

    o   The DiseaseColors argument in the plot.pigengene function can
	now be set automatically.

Bug Fixes

    o   pheatmap.type now works fine even when the number of samples in
	a condition is only 1.

                Changes in version 1.13.44 (2020-04-21)                 

Changes in existing functions

    o   one.step.pigengene now talks more, and automatically converts
	input data frames to matrices.

    o   module.heatmap now talks more, and does not get stuck if a
	module has only one gene, or if the expression levels of some
	genes in a module are not available in the data.

                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.