add_samples_controlgroup |
Add a sample to an existing control group |
as_control_group |
Convert list of nipt samples to nipt control group |
bin_bam_sample |
Load and bin BAM file |
calculate_ncv_score |
Use an NCV template to calculate a NCV score for sample of interest |
calculate_z_score |
Calculate 'standard' Z-score |
chi_correct |
Performs chi-square based variation reduction |
chrfractions |
Calculate chromosomal fraction |
diagnose_control_group |
Diagnose control group |
gc_correct |
Perform a GC bias correction on nipt sample |
getcontrolchromosomes |
Get control chromosomes names |
getfractionscontrolgroup |
Get all chromosomal fractions of a control group |
getreadscontrolgroup |
Get reads per chromosome per control group sample |
match_control_group |
Best matching control group by least sum of squares |
nipt_sample |
Load and bin BAM file |
perform_regression |
Regression based Z score |
prepare_ncv |
Prepare NCV calculation |
remove_duplicates_controlgroup |
Remove duplicate samples from control group |
remove_sample_controlgroup |
Remove a sample by samplename from control group |
retrieve_fractions_of_interest |
Retrieve the chromosomal fractions of a chromosome of interest |