R/calculate_intensity.R: cleaned the plotFeatures function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: First version of the groups object specific apply functions

The list object of MetaFeatures have 3 levels:
 1- groups
 2- experiments
 3- bamFiles

A group can contain 1 to n experiments. An experiment can contain 1 to n bam files.

applyOnGroups: To apply a function to every group in the list
applyOnExperiment: To apply a funciton to every experiment in the list
applyOnBamFiles: To apply a function to every bam files in the list

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Cleaning of the bootstrap functions

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Debugged the Merge Matrix step in plotFeatures

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Cleaned the bootstrap step from plotFeatures function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Merge branch 'master' of https://github.com/adeschen/MetaFeatures
R/calculate_intensity.R: fixed the return of bootstrapAnalysis function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Added plotGroups function in plotFeatures

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: corrected some minor bugs

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Splitted and debugged the plotting functions

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Removed deprecated functions and added missing comments

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>