NIPTeR (version 1.0.2)

calculate_z_score: Calculate 'standard' Z-score

Description

Calculate 'standard' Z-score

Usage

calculate_z_score(nipt_sample, nipt_control_group, chromo_focus)

Arguments

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

Value

ZscoreResult object

Details

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

Examples

## 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)