calculate_z_score: Calculate 'standard' Z-score
In NIPTeR: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal Testing

Description Usage Arguments Details Value Examples

Calculate 'standard' Z-score

1	calculate_z_score(nipt_sample, nipt_control_group, chromo_focus)

`nipt_sample`	The NIPTSample object that is the focus of the analysis
`nipt_control_group`	The NIPTControlGroup object used in the analysis
`chromo_focus`	The chromosome of interest. Most commonly chromosome 13, 18 or 21. However, every autosomal chromosome can be predicted

In the Z-score approach, introduced by Chiu et al in 2008, the chromosomal fraction of interest of a sample is compared to the chromosomal fractions of interest of the reference samples, the 'NIPTControlGroup' object. The output of the function is an object of class 'ZscoreResult'. It is a named list containing seven fields:

numeric sample_Zscore The Z score for the sample of interest for the sample of interest
named num control_group_statistics Named num of length 3, the first field being the mean (name mean), the second field is the standard deviation (name SD) and the third field is the P value of the Shapiro-Wilk test (name Shapiro_P_value)
matrix control_group_Zscores containing the Z scores of the chromosome of interest for all used control samples
integer focus_chromosome The chromosome of interest. Most commonly chromosome 13, 18 or 21. However, every autosomal chromosome can be predicted
string control_group_sample_names The sample names of all control group samples used in the analysis
string correction_status The correction status of the control group
string sample_name The sample_name of the sample of interest

ZscoreResult object

## Not run: 
z_score_result_13 <- calculate_z_score(nipt_sample = sample_of_interest, 
                                       nipt_control_group = control_group, 
                                       chromo_focus = 13)

## End(Not run)