In early development phase.
Developers: Tom Poorten, Randi Famula, Mitchell Feldmann
Functions to build:
- read in data - DONE
- filter SNPs - keep only polymorphic well-behaving (biallelic) SNPs
- make QAQC plots - sample-wise missing data distribution, ...?
- filter samples - by quality or vector of arbitrary sample IDs
- calc sample heterozygosity
- convert to GDS format for SNPRelate R package
- assess replicate samples and keep one sample per replicate set
- for expected reps - keep sample with best call rate
- for unexpected reps - keep sample that is pedigree-confirmed if possible
- pop structure viz - PCA
- flag unexpected PC values based on reported taxonomy
- pedigree analysis (IBD-based inference of PO relationships)