After the iNETgrate package was added to Bioconductor, Habil removed it from the Bitbucket and Github repositories.
In prepareSurvival and cleanAllData function,
the default values changes as follows: riskLow="Low" and
riskHigh="High", respectively.
The Labels argument is removed from analyzeSurvival.
and the riskCol argument is added.
The abnormalityCol argument is removed from accelFailAnalysis.
The otherLabel argument is removed from
prepareSurvival and cleanAllData functions.
The computeEigengenes, computeEigenloci, and
sample2atient functions were renamed to
computEigengenes, computEigenloci, and
sample2pat, respectively.
The makeNetwork function now saves the result for
each mu in a separate folder.
Data were compressed using "xz" to save 20% space.
The downloaData function is not exported anymore
because it is specific to the legacy TCGA data, which is no longer
available.
Habil renamed downloadData to downloaData
and updated the data.category argument of GDCquery.
Habil removed the legacy option from the donwlowData
function because it is no longer supported by TCGAbiolinks.
Habil commented the installation command line in the vignette.
Habil changed function names to camelCase i.e, from
function.name to functionName.
Habil changed getwd() to tempdr() in the docs.
Habil changed most of occurrences of cat() to paste().
Habil changed most of occurrences of print() to
message() or Pigengene::message.if().
Habil removed paste() inside all stop() to warning().
Habil replaced dontrun with donttest.
Tested on R 4.3.
TCGAbiolinks (<= 2.24.3) because of issues with newer versions.
Being prepared for submission to Bioconductor.
Created.