cbaf 1.0.0 - 2017-09-10
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New Functions:

- New availableData() functon to scan all the cancer studies to examine presence
  of RNA-seq, microRNA-seq, microarray(mRNA), microarray(miRNA) and methylation
  data.

- New obtainOneStudy() function to obtain and store the supported data for at
  least one group of genes across multiple subgroups of a cancer study. In
  addion, it can check whether or not all genes are included in different
  subgroups of a cancer study and, if not, looks for the alternative gene names.

- New obtainMultipleStudies() function to obtain and store the supported data
  for at least one group of genes across multiple cancer studies. It can check
  whether or not all genes are included in each cancer study and, if not, it
  looks for the alternative gene names.

- New automatedStatistics() function to calculate the statistics of the data
  obtained by obtainOneStudy() or obtainMultipleStudies() functions. Based
  on user's preference, these statistics can include frequency percentage,
  frequency ratio, mean value and median value of samples greater than specific
  value. Furthermore, it can look for the genes that comprise the highest values
  in each cancer and list the top 5 genes for frequency percentage, mean value
  and median value.

- New heatmapOutput() function to prepare heatmap for frequency percentage,
  mean value and  median value data provided by automatedStatistics() function.
  Heatmaps for every gene group are stored in separate folder.

- New xlsxOutput() function to export the output of automatedStatistics() and
  the gene validation result of one of the obtainOneStudy() or
  obtainMultipleStudies() functions as an excel file. For every gene group, an
  excel file will be generated and stored in the same folder as heatmaps.

- New cleanDatabase() function to remove the created databases in the cbaf
  package directory. This helps users to obtain the fresh data from
  cbioportal.org.

- New processOneStudy() function to combine obtainOneStudy(),
  automatedStatistics(), heatmapOutput() and xlsxOutput() functions for the ease
  of use.

- New processMultipleStudies() function to combine obtainMultipleStudies(),
  automatedStatistics(), heatmapOutput() and xlsxOutput() functions for the ease
  of use.