Man pages for seqminer
Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
| addJob | Add a job to a workflow |
| annotateGene | Annotate a test variant |
| annotatePlain | Annotate a plain text file |
| annotateVcf | Annotate a VCF file |
| createSingleChromosomeBCFIndex | Create a single chromosome index |
| createSingleChromosomeVCFIndex | Create a single chromosome index |
| download.annotation.resource | Download annotation resources to a directory |
| getCovPair | Extract pair of positions by ranges |
| getRefBase | Annotate a test variant |
| hasIndex | Check input file has tabix index |
| isDirWritable | Test whether directory is writable |
| isInRange | Test whether a vector of positions are inside given ranges |
| isTabixRange | Check if the inputs are valid tabix range such as chr1:2-300 |
| isURL | Check if the input is url e.g. http:// or ftp:// |
| makeAnnotationParameter | Construct a usable set of annotation parameters |
| newJob | Create a new job |
| newWorkflow | Create a new workflow |
| openPlink | Open binary PLINK files |
| readBGENToListByGene | Read information from BGEN file in a given range and return a... |
| readBGENToListByRange | Read information from BGEN file in a given range and return a... |
| readBGENToMatrixByGene | Read a gene from BGEN file and return a genotype matrix |
| readBGENToMatrixByRange | Read a gene from BGEN file and return a genotype matrix |
| readPlinkToMatrixByIndex | Read from binary PLINK file and return a genotype matrix |
| readSingleChromosomeBCFToMatrixByRange | Read a range from BCF file and return a genotype matrix |
| readSingleChromosomeVCFToMatrixByRange | Read a range from VCF file and return a genotype matrix |
| readVCFToListByGene | Read information from VCF file in a given range and return a... |
| readVCFToListByRange | Read information from VCF file in a given range and return a... |
| readVCFToMatrixByGene | Read a gene from VCF file and return a genotype matrix |
| readVCFToMatrixByRange | Read a gene from VCF file and return a genotype matrix |
| rvmeta.readCovByRange | Read covariance by range from METAL-format files. |
| rvmeta.readDataByGene | Read association statistics by gene from METAL-format files.... |
| rvmeta.readDataByRange | Read association statistics by range from METAL-format files.... |
| rvmeta.readNullModel | Read null model statistics |
| rvmeta.readScoreByRange | Read score test statistics by range from METAL-format files. |
| rvmeta.readSkewByRange | Read skew by range from METAL-format files. |
| rvmeta.writeCovData | Write covariance association statistics files. |
| rvmeta.writeScoreData | Write score-based association statistics files. |
| SEQMINER | Efficiently Read Sequencing Data (VCF format, METAL format)... |
| sub-.PlinkFile | Read from binary PLINK file and return a genotype matrix |
| tabix.createIndex | Create tabix index file, similar to running tabix in command... |
| tabix.createIndex.meta | Create tabix index for bgzipped MetaScore/MetaCov file |
| tabix.createIndex.vcf | Create tabix index for bgzipped VCF file |
| tabix.read | Read tabix file, similar to running tabix in command line. |
| tabix.read.header | Read tabix file, similar to running tabix in command line. |
| tabix.read.table | Read tabix file, similar to running tabix in command line. |
| validateAnnotationParameter | Validate annotate parameter is valid |
| verifyFilename | validate the inVcf can be created, and outVcf can be write... |
| writeWorkflow | Export workflow to Makefile |
