Package: seqminer 9.7

Xiaowei Zhan

seqminer: 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.

Authors:Xiaowei Zhan [aut, cre], Dajiang Liu [aut], Attractive Chaos [cph], Broad Institute / Massachusetts Institute of Technology [cph], Genome Research Ltd [cph], Facebook, Inc [cph], D. Richard Hipp [cph]

seqminer_9.7.tar.gz
seqminer_9.7.tar.gz(r-4.5-noble)seqminer_9.7.tar.gz(r-4.4-noble)
seqminer.pdf |seqminer.html✨
seqminer/json (API)

# Install 'seqminer' in R:
install.packages('seqminer', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/zhanxw/seqminer/issues

Uses libs:
  • zlib– Compression library
  • bzip2– High-quality block-sorting file compressor library
  • libzstd– Fast lossless compression algorithm
  • sqlite3– SQLite 3 shared library
  • c++– GNU Standard C++ Library v3

zlibbzip2libzstdsqlite3cpp

5.09 score 6 packages 111 scripts 1.0k downloads 4 mentions 41 exports 0 dependencies

Last updated 3 months agofrom:50eb26ef79. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 02 2024
R-4.5-linux-x86_64OKDec 02 2024

Exports:addJobannotateGeneannotatePlainannotateVcfcreateSingleChromosomeBCFIndexcreateSingleChromosomeVCFIndexdownload.annotation.resourcegetRefBaseisInRangeisTabixRangemakeAnnotationParameternewJobnewWorkflowopenPlinkreadBGENToListByGenereadBGENToListByRangereadBGENToMatrixByGenereadBGENToMatrixByRangereadPlinkToMatrixByIndexreadSingleChromosomeBCFToMatrixByRangereadSingleChromosomeVCFToMatrixByRangereadVCFToListByGenereadVCFToListByRangereadVCFToMatrixByGenereadVCFToMatrixByRangervmeta.readCovByRangervmeta.readDataByGenervmeta.readDataByRangervmeta.readNullModelrvmeta.readScoreByRangervmeta.readSkewByRangervmeta.writeCovDatarvmeta.writeScoreDatatabix.createIndextabix.createIndex.metatabix.createIndex.vcftabix.readtabix.read.headertabix.read.tablevalidateAnnotationParameterwriteWorkflow

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Read from binary PLINK file and return a genotype matrix[.PlinkFile
Add a job to a workflowaddJob
Annotate a test variantannotateGene
Annotate a plain text fileannotatePlain
Annotate a VCF fileannotateVcf
Create a single chromosome indexcreateSingleChromosomeBCFIndex
Create a single chromosome indexcreateSingleChromosomeVCFIndex
Download annotation resources to a directorydownload.annotation.resource
Extract pair of positions by rangesgetCovPair
Annotate a test variantgetRefBase
Test whether directory is writableisDirWritable
Test whether a vector of positions are inside given rangesisInRange
Check if the inputs are valid tabix range such as chr1:2-300isTabixRange
Construct a usable set of annotation parametersmakeAnnotationParameter
Create a new jobnewJob
Create a new workflownewWorkflow
Open binary PLINK filesopenPlink
Read information from BGEN file in a given range and return a listreadBGENToListByGene
Read information from BGEN file in a given range and return a listreadBGENToListByRange
Read a gene from BGEN file and return a genotype matrixreadBGENToMatrixByGene
Read a gene from BGEN file and return a genotype matrixreadBGENToMatrixByRange
Read from binary PLINK file and return a genotype matrixreadPlinkToMatrixByIndex
Read a range from BCF file and return a genotype matrixreadSingleChromosomeBCFToMatrixByRange
Read a range from VCF file and return a genotype matrixreadSingleChromosomeVCFToMatrixByRange
Read information from VCF file in a given range and return a listreadVCFToListByGene
Read information from VCF file in a given range and return a listreadVCFToListByRange
Read a gene from VCF file and return a genotype matrixreadVCFToMatrixByGene
Read a gene from VCF file and return a genotype matrixreadVCFToMatrixByRange
Read covariance by range from METAL-format files.rvmeta.readCovByRange
Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted.rvmeta.readDataByGene
Read association statistics by range from METAL-format files. Both score statistics and covariance statistics will be extracted.rvmeta.readDataByRange
Read null model statisticsrvmeta.readNullModel
Read score test statistics by range from METAL-format files.rvmeta.readScoreByRange
Read skew by range from METAL-format files.rvmeta.readSkewByRange
Write covariance association statistics files.rvmeta.writeCovData
Write score-based association statistics files.rvmeta.writeScoreData
Efficiently Read Sequencing Data (VCF format, METAL format) into Rseqminer-package seqminer
Create tabix index file, similar to running tabix in command line.tabix.createIndex
Create tabix index for bgzipped MetaScore/MetaCov filetabix.createIndex.meta
Create tabix index for bgzipped VCF filetabix.createIndex.vcf
Read tabix file, similar to running tabix in command line.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
Validate annotate parameter is validvalidateAnnotationParameter
validate the inVcf can be created, and outVcf can be write to. will stop if any error occursverifyFilename
Export workflow to MakefilewriteWorkflow