Function reference • RAIDS

All functions
`RAIDS-package` `RAIDS`	RAIDS: Accurate Inference of Genetic Ancestry from Cancer Sequences
`add1KG2SampleGDS()`	Add the genotype information for the list of pruned SNVs into the Profile GDS file
`addGeneBlockGDSRefAnnot()`	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
`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.
`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
`getRef1KGPop()`	Extract the specified column 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
`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
`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

Reference

All functions