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

Build Status AppVeyor build status CRAN_Status_Badge

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:

Zhan, X. and Liu, D. J. (2015), SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations. Genet. Epidemiol., 39: 619–623. doi:10.1002/gepi.21918

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 (MIT license), SQLite (Public Domain), Zstandard (MIT license). For tabix, we removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics. For zstandard, we removed compiler (clang, MSVC) specific preprocessing flags.
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

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