Specific comments lacking for parameters hard-coded within cnvAnalysis.R

[andrewdavidsmith]

The following is not sufficient:

# CONSTANTS
## Parameters as in 'Baslan, Timour, et al. "Genome-wide copy number analysis of single
## cells." Nature protocols 7.6 (2012): 1024.'
kAlphaValue  <- 0.02
kNPermutations  <- 1000
kStandardDev <- 0.5
kMinWidth <- 4

We need to have a description of these 4 parameters. Doesn't have to be too long, but right now a reader (or user) would not have any idea what they are doing without scrutinizing the original paper.

[rishvanth-kp]

Added a brief description for constants.

  # CONSTANTS
  ## Number of permutations for p-value computation
  kNPermutations  <- 1000 
  ## Significance level for the test to accept segment change points
  kAlphaValue  <- 0.02
  ## Number of standard deviations between mean ratio to keep a segment
  kStandardDev <- 0.5
  ## Minimum number of bins for a changed segment
  kMinWidth <- 4