# Accurate Inference of Genetic Ancestry from Cancer Sequences

## Documentation for package ‘RAIDS’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add1KG2SampleGDS | Add the genotype information for the list of pruned SNVs into the Profile GDS file
addBlockFromDetFile | Append information associated to ld blocks, as indexes, into the Population Reference SNV Annotation GDS file
addGeneBlockGDSRefAnnot | Append information associated to blocks, as indexes, into the Population Reference SNV Annotation GDS file
addGeneBlockRefAnnot | Append information associated to blocks, as indexes, into the Population Reference SNV Annotation GDS file
addRef2GDS1KG | Add the information about the unrelated patients to the Reference GDS file
addStudy1Kg | Append information about the 1KG samples into the Profile GDS file
computeAncestryFromSynthetic | Select the optimal K and D parameters using the synthetic data and infer the ancestry of a specific profile
computeAncestryFromSyntheticFile | Select the optimal K and D parameters using the synthetic data and infer the ancestry of a specific profile
computeKNNRefSample | Run a k-nearest neighbors analysis on one specific profile
computeKNNRefSynthetic | Run a k-nearest neighbors analysis on a subset of the synthetic dataset
computePCAMultiSynthetic | Project synthetic profiles onto existing principal component axes generated using the reference 1KG profiles
computePCARefSample | Project specified profile onto PCA axes generated using known reference profiles
computePoolSyntheticAncestryGr | Run a PCA analysis and a K-nearest neighbors analysis on a small set of synthetic data using all 1KG profiles except the ones used to generate the synthetic profiles
computeSyntheticROC | Calculate the AUROC of the inferences for specific values of D and K using the inferred ancestry results from the synthetic profiles.
createAccuracyGraph | Generate accuracy graph
createAUROCGraph | Generate accuracy graph
createStudy2GDS1KG | Create the Profile GDS file(s) for one or multiple specific profiles using the information from a RDS Sample description file and the 1KG GDS file
demoKnownSuperPop1KG | The known super population ancestry of the demo 1KG reference profiles.
demoPCA1KG | The PCA results of the demo 1KG reference dataset for demonstration purpose. Beware that the PCA has been run on a very small subset of the 1KG reference dataset and should not be used to call ancestry inference on a real profile.
demoPCASyntheticProfiles | The PCA result of demo synthetic profiles projected on the demo subset 1KG reference PCA.
demoPedigreeEx1 | The pedigree information about a demo profile called 'ex1'.
estimateAllelicFraction | Estimate the allelic fraction of the pruned SNVs for a specific profile
generateGDS1KG | Generate the GDS file that will contain the information from Reference data set (reference data set)
generateMapSnvSel | Generate the filter SNP information file in RDS format
generatePhase1KG2GDS | Adding the phase information into the Reference GDS file
generatePhaseRef | Adding the phase information into the Reference GDS file
getRef1KGPop | Extract the specified column from the 1KG GDS 'sample.ref' node for the reference profiles (real ancestry assignation)
getRefSuperPop | Extract the from the 1KG GDS 'sample.ref' node for the reference profiles (real ancestry assignation)
groupChr1KGSNV | Merge the genotyping files per chromosome into one file
identifyRelative | Identify genetically unrelated patients in GDS Reference file
identifyRelativeRef | Identify genetically unrelated patients in GDS Reference file
inferAncestry | Run most steps leading to the ancestry inference call on a specific DNA profile
inferAncestryGeneAware | Run most steps leading to the ancestry inference call on a specific RNA profile
matKNNSynthetic | A small 'data.frame' containing the inferred ancestry on the synthetic profiles.
pedSynthetic | A small 'data.frame' containing the information related to synthetic profiles. The ancestry of the profiles used to generate the synthetic profiles must be present.
prepPed1KG | Prepare the pedigree file using pedigree information from Reference
prepSynthetic | Add information related to the synthetic profiles (study and synthetic reference profiles information) into a Profile GDS file
pruningSample | Compute the list of pruned SNVs for a specific profile using the information from the Reference GDS file and a linkage disequilibrium analysis
runExomeAncestry | Run most steps leading to the ancestry inference call on a specific exome profile
runRNAAncestry | Run most steps leading to the ancestry inference call on a specific RNA profile
select1KGPop | Random selection of a specific number of reference profiles in each subcontinental population present in the 1KG GDS file
select1KGPopForSynthetic | Random selection of a specific number of reference profiles in each subcontinental population present in the 1KG GDS file ( same as select1KGPop but the function doesn't need gds object as parameters but the file name of the referenceGDS )
snpPositionDemo | A small 'data.frame' containing the SNV information.
snvListVCF | Generate a VCF with the information from the SNPs that pass a cut-off threshold
splitSelectByPop | Group samples per subcontinental population
syntheticGeno | Generate synthetic profiles for each cancer profile and 1KG reference profile combination and add them to the Profile GDS file