NIPTeR (version 1.0.2)

match_control_group: Best matching control group by least sum of squares

Description

The matchcontrolgroup function determines how well an NIPTSample fits within the NIPTControlGroup

Usage

match_control_group(nipt_sample, nipt_control_group, mode, n_of_samples, include_chromosomes = NULL, exclude_chromosomes = NULL)

Arguments

nipt_sample

The NIPTSample object that is the focus of the analysis

nipt_control_group

The NIPTControlGroup object used in the analysis

mode

The function mode. This can either be "subset" or "report". Mode "subset" means the return value will be a new `NIPTControlGroup` object containing n samples. When mode "report" is used the output is a matrix containing the sum of squares score of the differences between the chromosomal fractions of the sample and the control for every control sample, sorted in increasing score.

n_of_samples

The length of the resulting NIPTControlGroup. Only applicable if mode "subset" is used.

include_chromosomes

integer. Include potential trisomic chromosomes into the comparison? Default = NULL, meaning chromosomes 13, 18 and 21 are not included

exclude_chromosomes

integer.Exclude other autosomal chromosomes besides chromosomes 13, 18 and 21? Default = NULL

Value

The output for mode subset is a new `NIPTControlGroup` composed of _n_ samples. The output for mode report is a matrix with a single column containing the sum of squares in ascending order.

Details

The `matchcontrolgroup` function determines how well an NIPTSample fits within the NIPTControlGroup and, if needed, makes a subset `NIPTControlGroup` of length n.

Examples

## Not run: 
# ##Mode report
# scores_control_group <- matchcontrolgroup(nipt_sample = sample_of_interest, 
#                                           nipt_control_group = control_group, 
#                                           mode = "report", include_chromosomes = c(13,18))
# 
# ##Mode subset
# subset_control_group <- matchcontrolgroup(nipt_sample = sample_of_interest, 
#                                           nipt_control_group = control_group, 
#                                           mode = "subset", n_of_samples = 50)
# ## End(Not run)