NIPTeR: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal Testing
Version 1.0.2

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

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AuthorDirk de Weerd, Lennart Johansson
Date of publication2016-03-09 18:55:22
MaintainerLennart Johansson <l.johansson@umcg.nl>
LicenseGNU Lesser General Public License
Version1.0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("NIPTeR")

Man pages

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...
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
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...

Functions

BuildFullModel Source code
CalculateVariation Source code
CorrectGcWithWeights Source code
GetCorrectionFactor Source code
GetMeanNumberOfReadsGcStep Source code
GetNextPredictor Source code
PredictTrisomy Source code
RetrieveSubsets Source code
SelectModelsFixedRegressionApproach Source code
SelectModelsFixedRegressionApproach.CombinedStrands Source code
SelectModelsFixedRegressionApproach.SeparatedStrands Source code
ZScoresControl Source code
add_samples_controlgroup Man page Source code
appendchromosomes Source code
as_control_group Man page Source code
bin_bam_sample Man page Source code
bin_reads Source code
calculate_ncv_score Man page Source code
calculate_regression_scores Source code
calculate_z_score Man page Source code
chi_correct Man page Source code
chrfractions Man page Source code
chrfractions.CombinedStrands Source code
chrfractions.SeparatedStrands Source code
chrreads Source code
collapse_all_stats Source code
collapse_prac_cv_control_scores Source code
collapse_prediction_sets Source code
collapse_result Source code
collapse_results Source code
construct_sample Source code
correct.reads Source code
correct_reads_sex_chromosome Source code
correct_sample_bin Source code
correct_sample_loess Source code
correctbins Source code
correctsamples Source code
correctsamples_include_xy Source code
diagnose_control_group Man page Source code
gc_correct Man page Source code
gc_correct_NIPTControlGroup_bin Source code
gc_correct_NIPTControlGroup_loess Source code
gc_correct_NIPTSample_bin Source code
gc_correct_NIPTSample_loess Source code
get_abberant_scores Source code
get_mean_sd_shapiro Source code
get_ncv_reads Source code
get_ncv_statistics Source code
getbins Source code
getcontrolchromosomes Man page Source code
getcontrolchromosomes.CombinedStrands Source code
getcontrolchromosomes.SeparatedStrands Source code
getcorrectionstatus Source code
getfractionscontrolgroup Man page Source code
getfractionscontrolgroup.CombinedStrands Source code
getfractionscontrolgroup.SeparatedStrands Source code
getreadscontrolgroup Man page Source code
getreadscontrolgroup.CombinedStrands Source code
getreadscontrolgroup.SeparatedStrands Source code
getsamplenames Source code
getstats Source code
getstrandtype Source code
listmodels Source code
match_control_group Man page Source code
mean_correction Source code
ncv_template Source code
nipt_sample Man page
perform_regression Man page Source code
prepare_ncv Man page Source code
regression_template Source code
remove_duplicates_controlgroup Man page Source code
remove_sample_controlgroup Man page Source code
retrieve_fractions_of_interest Man page Source code
retrieve_fractions_of_interest.CombinedStrands Source code
retrieve_fractions_of_interest.SeparatedStrands Source code
rownames_additional_stats Source code
setrownamesmatrix Source code
splitchromosomes Source code
sumchiscores Source code
sumfandrautosomal Source code
sumfandrsex Source code
testtrainset Source code
unlist Source code
z_score_template Source code

Files

inst
inst/doc
inst/doc/NIPTeR.R
inst/doc/NIPTeR.html
inst/doc/NIPTeR.Rmd
NAMESPACE
R
R/bin_sample.R
R/regression_result.R
R/regression.R
R/general_functions.R
R/sysdata.rda
R/bin_gc_correct.R
R/Sample.R
R/best_fit_beta.R
R/prepare_ncv_template.R
R/diagnose_control_group.R
R/chi_correction.R
R/z_score.R
R/gc_correct_distribute.R
R/ncv_calculation.R
R/control_group.R
R/constants.R
R/ncv_template.R
R/gc_correct.R
vignettes
vignettes/figures
vignettes/figures/simple_workflow.png
vignettes/figures/complex_workflow.png
vignettes/figures/control_group_workflow.png
vignettes/NIPTeR.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/remove_sample_controlgroup.Rd
man/retrieve_fractions_of_interest.Rd
man/calculate_z_score.Rd
man/add_samples_controlgroup.Rd
man/as_control_group.Rd
man/gc_correct.Rd
man/getcontrolchromosomes.Rd
man/getreadscontrolgroup.Rd
man/remove_duplicates_controlgroup.Rd
man/getfractionscontrolgroup.Rd
man/chrfractions.Rd
man/match_control_group.Rd
man/prepare_ncv.Rd
man/diagnose_control_group.Rd
man/bin_bam_sample.Rd
man/calculate_ncv_score.Rd
man/perform_regression.Rd
man/chi_correct.Rd
NIPTeR documentation built on May 19, 2017, 8:20 p.m.