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

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

Author
Dirk de Weerd, Lennart Johansson
Date of publication
2016-03-09 18:55:22
Maintainer
Lennart Johansson <l.johansson@umcg.nl>
License
GNU Lesser General Public License
Version
1.0.2

View on CRAN

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...

Files in this package

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