NIPTeR (version 1.0.2)

Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal Testing

Description

Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal Testing.

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Version

Install

install.packages('NIPTeR')

Monthly Downloads

160

Version

1.0.2

License

GNU Lesser General Public License

Maintainer

Lennart Johansson

Last Published

March 9th, 2016

Functions in NIPTeR (1.0.2)

retrieve_fractions_of_interest

Retrieve the chromosomal fractions of a chromosome of interest

diagnose_control_group

Diagnose control group

bin_bam_sample

Load and bin BAM file

match_control_group

Best matching control group by least sum of squares

calculate_ncv_score

Use an NCV template to calculate a NCV score for sample of interest

gc_correct

Perform a GC bias correction on nipt sample

perform_regression

Regression based Z score

remove_duplicates_controlgroup

Remove duplicate samples from control group

calculate_z_score

Calculate 'standard' Z-score

chrfractions

Calculate chromosomal fraction

chi_correct

Performs chi-square based variation reduction

as_control_group

Convert list of nipt samples to nipt control group

getreadscontrolgroup

Get reads per chromosome per control group sample

add_samples_controlgroup

Add a sample to an existing control group

getcontrolchromosomes

Get control chromosomes names

remove_sample_controlgroup

Remove a sample by samplename from control group

getfractionscontrolgroup

Get all chromosomal fractions of a control group

prepare_ncv

Prepare NCV calculation