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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:

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

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Version

Install

install.packages('seqminer')

Monthly Downloads

727

Version

6.7

License

GPL | file LICENSE

Maintainer

Xiaowei Zhan

Last Published

December 6th, 2018

Functions in seqminer (6.7)

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

Extract pair of positions by ranges

Annotate a test variant

Create a new job

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.

Efficiently Read Sequencing Data (VCF format, METAL format) into R

Add a job to a workflow

Test whether a vector of positions are inside given ranges

Annotate a test variant

Annotate a VCF file

Check if the inputs are valid tabix range such as chr1:2-300

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.

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

validate the inVcf can be created, and outVcf can be write to. will stop if any error occurs

Export workflow to Makefile

readVCFToListByGene

Read information from VCF file in a given range and return a list

Test whether directory is writable

Check if the input is url e.g. http:// or ftp://

makeAnnotationParameter

Construct a usable set of annotation parameters