seqminer v7.1
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Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Readme
SEQMINER
Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R
Quick introduction is available: [http://seqminer.genomic.codes/].
Install the latest stable version:
install.packages("seqminer")
Install the development version (devtools package is required):
devtools::install_github("zhanxw/seqminer")
Citation:
Functions in seqminer
| Name | Description | |
| getCovPair | Extract pair of positions by ranges | |
| annotateGene | Annotate a test variant | |
| getRefBase | Annotate a test variant | |
| hasIndex | Check input file has tabix index | |
| newJob | Create a new job | |
| newWorkflow | Create a new workflow | |
| annotateVcf | Annotate a VCF file | |
| isDirWritable | Test whether directory is writable | |
| download.annotation.resource | Download annotation resources to a directory | |
| readVCFToMatrixByGene | Read a gene from VCF file and return a genotype matrix | |
| annotatePlain | Annotate a plain text file | |
| isInRange | Test whether a vector of positions are inside given ranges | |
| readVCFToMatrixByRange | Read a gene from VCF file and return a genotype matrix | |
| 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. | |
| isTabixRange | Check if the inputs are valid tabix range such as chr1:2-300 | |
| rvmeta.readCovByRange | Read covariance by range from METAL-format files. | |
| isURL | Check if the input is url e.g. http:// or ftp:// | |
| verifyFilename | validate the inVcf can be created, and outVcf can be write to. will stop if any error occurs | |
| openPlink | Open binary PLINK files | |
| rvmeta.readDataByGene | Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted. | |
| makeAnnotationParameter | Construct a usable set of annotation parameters | |
| rvmeta.readDataByRange | Read association statistics by range from METAL-format files. Both score statistics and covariance statistics will be extracted. | |
| writeWorkflow | Export workflow to Makefile | |
| tabix.createIndex.meta | Create tabix index for bgzipped MetaScore/MetaCov file | |
| tabix.createIndex.vcf | Create tabix index for bgzipped VCF file | |
| SeqMiner | Efficiently Read Sequencing Data (VCF format, METAL format) into R | |
| addJob | Add a job to a workflow | |
| readBGENToListByRange | Read information from BGEN file in a given range and return a list | |
| readBGENToMatrixByRange | Read a gene from BGEN file and return a genotype matrix | |
| readBGENToListByGene | Read information from BGEN file in a given range and return a list | |
| readPlinkToMatrixByIndex | Read a gene from BGEN file and return a genotype matrix | |
| rvmeta.readNullModel | Read null model statistics | |
| rvmeta.readScoreByRange | Read score test statistics by range from METAL-format files. | |
| [.PlinkFile | Read a gene from BGEN file and return a genotype matrix | |
| rvmeta.readSkewByRange | Read skew by range from METAL-format files. | |
| tabix.createIndex | Create tabix index file, similar to running tabix in command line. | |
| tabix.read.table | Read tabix file, similar to running tabix in command line. | |
| readVCFToListByGene | Read information from VCF file in a given range and return a list | |
| readBGENToMatrixByGene | Read a gene from BGEN file and return a genotype matrix | |
| readVCFToListByRange | Read information from VCF file in a given range and return a list | |
| rvmeta.writeCovData | Write covariance association statistics files. | |
| validateAnnotationParameter | Validate annotate parameter is valid | |
| rvmeta.writeScoreData | Write score-based association statistics files. | |
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Details
| Type | Package |
| Date | 2019-1-7 |
| Copyright | We have used the following software and made minimal
necessary changes: tabix, Heng Li |
| License | GPL | file LICENSE |
| URL | http://seqminer.genomic.codes |
| BugReports | https://github.com/zhanxw/seqminer/issues |
| Packaged | 2019-01-07 21:30:23 UTC; zhanxw |
| Repository | CRAN |
| SystemRequirements | C++11, zlib headers and libraries, GNU make, optionally also bzip2 and POSIX-compliant regex functions. |
| NeedsCompilation | yes |
| RoxygenNote | 6.1.1 |
| Encoding | UTF-8 |
| Date/Publication | 2019-01-08 15:20:03 UTC |
| suggests | SKAT , testthat |
| Contributors | Dajiang Liu, Broad Institute / Massachusetts Institute of Technology, Genome Research Ltd (GRL), Attractive Chaos , Facebook, Inc |
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