snpStats

[tuxette]

• [ ] check why NA's indices are only returned in the case of a class different from dgCMatrix
• [ ] check if a warning must be added when the diagonal is not (from scratch) equal to 1
• [ ] non uniform treatment for different types of input

[pneuvial]

• [x] check why NA's indices are only returned in the case of a class different from dgCMatrix

because in this case the input is assumed to be a matrix of genotypes (as now made more explicit in the documentation of snpClust. The LD is calculated internally and not returned, so we found useful to report the indices for the NA values in this specific case

• [x] check if a warning must be added when the diagonal is not (from scratch) equal to 1

Added such a warning (only for dgCMatrix). Updated tests accordingly.

• [x] non uniform treatment for different types of input

i.e. dgCMatrix is assumed to be a (LD) similarity matrix, while the other types of inputs are assumed to be a matrix of genotypes. Not changed (but clarified in the documentation of snpClust.