R/calculate_intensity.R: In parseRegins function, an incorrect argument name was used when calling the scaleVectors function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Solved a bug in prepareRegions function where chromosome names were loaded as factor instead of characters

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Solved a bug in prepareRegions function that caused the removeControls function to return incorrect design when there was no design file

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
vignettes/MetaFeatures.Rmd: Removed the cache=TRUE chunk argument used in a few R code block

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Added examples in the man files of every functions

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