seqminer v6.7

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

Type Package
Date 2018-12-04
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 2018-12-04 16:32:59 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 2018-12-06 22:10:04 UTC

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