The current input format for the c3co function involves a list of data.frames with 4 columns (total CN, DH, position, chromosome), and an argument 'stat' to explicitly specify whether to work on total CN only or jointly on total CN, DH :
function (dat, stat = c("C1C2", "TCN"), ...)
This is redundant (position and chromosome should be the same for all elements of the list)
It's not obious to apply the function when DH is not available (one has to add a dummy 'DH' column to all the elements in the list
(related) the position information is currently not used
It seems to me that a more efficient and user-friendly signature for this function would be:
function (CN, DH=NULL, chromosome=NULL, position=NULL, ...)
where :
'CN' is a numeric matrix
'DH' is an optional numeric matrix (if not provided, c3co is run on CN only)
'chromosome' is an optional vector (if not provided, we assume one chromosome)
'position' is an optional vector (if not provided, we assume that the input data are already sorted)
jchiquet
commented
7 years ago
The current input format for the
c3cofunction involves a list of data.frames with 4 columns (total CN, DH, position, chromosome), and an argument 'stat' to explicitly specify whether to work on total CN only or jointly on total CN, DH :It seems to me that a more efficient and user-friendly signature for this function would be:
where :