Man pages for hapFabia
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
| analyzeIBDsegments | Loop over extracted IBD segments to supply a descriptive... |
| chr1ASW1000G | Example genotype data in 'vcf' format |
| compareIBDsegmentLists | Hierarchical clustering of IBD segments stored in IBD segment... |
| extractIBDsegments | Extract IBD segments from a 'fabia' result |
| findDenseRegions | Find accumulations of values via histogram counts |
| hapFabia | IBD segment extraction by FABIA |
| hapFabiaVersion | Display version info for package 'hapFabia' |
| hapRes | Example result of 'hapFabia' |
| IBDsegment-class | IBDsegment instances and methods |
| IBDsegmentList2excel | Store an IBD segment list in EXCEL / csv format |
| IBDsegmentList-class | IBDsegmentList instances and methods |
| identifyDuplicates | Identify duplicates of IBD segments |
| iterateIntervals | Loop over DNA intervals with a call of 'hapFabia' |
| makePipelineFile | Generate 'pipleline.R' |
| matrixPlot | Basic plot function for IBD segments |
| mergedIBDsegmentList | Example IBD segment list as a result of 'hapFabia' |
| mergeIBDsegmentLists | Merging IBD segments |
| plotIBDsegment | Plots an IBD segment given genotype data and tagSNVs |
| res | Example result of 'spfabia' |
| setAnnotation | Fills in annotations of tagSNVs of a list of IBD segments |
| setStatistics | Computes and stores the statistics of an IBD segment list |
| sim | Similarity measures for IBD segments |
| simu | Example simulation data for 'hapFabia' |
| simulateIBDsegments | Generates simulated genotyping data with IBD segments |
| simulateIBDsegmentsFabia | Generates simulated genotyping data with IBD segments for... |
| split_sparse_matrix | Splits genotyping data in sparse matrix format into intervals |
| toolsFactorizationClass | Tools to analyze results of 'fabia' |
| vcftoFABIA | Converting genotyping data from 'vcf' to sparse matrix format |
