Man pages for belleau/aicsPaper
Accurate Inference of Genetic Ancestry from Cancer Sequencing
| add1KG2SampleGDS | TODO |
| addBlockFromPlink2GDS | TODO contain the information from 1KG |
| addGDS1KGLDBlock | TODO |
| addGDSRef | The function add an array sample.ref to the gds file.It... |
| addGDSStudyPruning | fill the pruned.study in the gds file |
| addPhase1KG2SampleGDSFromFile | TODO |
| addPhase1KG2SampleGDSFromGDS | TODO |
| addRef2GDS1KG | Add the information about the unrelated patients to the GDS... |
| addStudy1Kg | TODO |
| addStudyGDSSample | This function create the gds file fields related to the study... |
| addUpdateLap | TODO |
| addUpdateSegment | TODO |
| appendGDSgenotype | This function append the field genotype in the gds file |
| appendGDSgenotypeMat | This function append the field genotype in the gds file |
| appendGDSSample | This function append the fields related to the samples. If... |
| appendGDSSampleOnly | This function append the fields sample.id. |
| appendStudy2GDS1KG | Create a study at GDS including the reference (first study... |
| basePCASample | TODO |
| computeAlleleFraction | TODO |
| computeAllelicFractionDNA | TODO |
| computeAllelicImbDNAChr | TODO |
| computeKNNSuperPoprSynthetic | TODO |
| computeLOHBlocksDNAChr | TODO |
| computePCAForSamples | Project patients onto existing principal component axes (PCA) |
| computePCAsynthetic | TODO |
| computePrunedPCARef | Compute principal component axes (PCA) on pruned SNV with the... |
| computeSyntheticConfMat | TODO |
| computeSyntheticROC | TODO |
| estimateAllelicFraction | TODO |
| gds2tfam | create a file tfam file for plink from the gds file |
| gds2tfamSample | create a file tfam file for plink from the gds file |
| gds2tped | create a file tped file for plink from the gds file |
| generateGDS1KG | Generate the GDS file that will contain the information from... |
| generateGDS1KGgenotypeFromSNPPileup | TODO This function append the genotype and the file related... |
| generateGDSgenotype | This function create the field genotype in the gds file |
| generateGDSSample | Initialization of the section related to the sample... |
| generateGDSSNPinfo | This function create the fields related to the snp |
| generateMapSnvSel | Generate the filter SNP information file in RDS format |
| generatePhase1KG2GDS | TODO |
| getTableSNV | TODO |
| groupChr1KGSNV | Merge the genotyping files per chromosome into one file |
| groupChrPruning | Merge the pruning files by chromosome in one file |
| identifyRelative | Identify genetically unrelated patients in GDS 1KG file |
| prepPed1KG | Prepare the pedigree file using pedigree information from 1KG |
| prepPedSynthetic1KG | TODO |
| prepSynthetic | TODO |
| processBlockChr | TODO |
| projectSample2PCA | Project patients onto existing principal component axes (PCA) |
| pruning1KG.Chr | Find the pruned snv in 1KG by chr |
| pruningSample | TODO |
| RAIDS-package | RAIDS: Ancestry Inference from Cancer Sequencing |
| runIBDKING | Function just wrap snpgdsIBDKING |
| runLDPruning | TODO just a wrapper of snpgdsLDpruning |
| select1KGPop | TODO |
| selParaPCAUpQuartile | TODO |
| snvListVCF | Generate a VCF with the information from the SNPs that pass a... |
| syntheticGeno | TODO |
| testAlleleFractionChange | TODO |
| testEmptyBox | TODO |
