Accurate Inference of Genetic Ancestry from Cancer Sequences

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Documentation for package ‘RAIDS’ version 1.5.0

• 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