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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

7.1

License

GPL | file LICENSE

Maintainer

Xiaowei Zhan

Last Published

January 8th, 2019

Functions in seqminer (7.1)

Extract pair of positions by ranges

Annotate a test variant

Annotate a test variant

Check input file has tabix index

Create a new job

Create a new workflow

Annotate a VCF file

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

Annotate a plain text file

Test whether a vector of positions are inside given ranges

readVCFToMatrixByRange

Read a gene from VCF file and return a genotype matrix

Read tabix file, similar to running tabix in command line.

tabix.read.header

Read tabix file, similar to running tabix in command line.

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

rvmeta.readCovByRange

Read covariance by range from METAL-format files.

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

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

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.

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

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

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.

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.