Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Add a job to a workflow
Annotate a test variant
Annotate a plain text file
Annotate a VCF file
Create a single chromosome index
Create a single chromosome index
Download annotation resources to a directory
Extract pair of positions by ranges
Annotate a test variant
Check input file has tabix index
Test whether directory is writable
Test whether a vector of positions are inside given ranges
Check if the inputs are valid tabix range such as chr1:2-300
Check if the input is url e.g. http:// or ftp://
Construct a usable set of annotation parameters
Create a new job
Create a new workflow
Open binary PLINK files
Read information from BGEN file in a given range and return a list
Read information from BGEN file in a given range and return a list
Read a gene from BGEN file and return a genotype matrix
Read a gene from BGEN file and return a genotype matrix
Read from binary PLINK file and return a genotype matrix
Read a range from BCF file and return a genotype matrix
Read a range from VCF file and return a genotype matrix
Read information from VCF file in a given range and return a list
Read information from VCF file in a given range and return a list
Read a gene from VCF file and return a genotype matrix
Read a gene from VCF file and return a genotype matrix
Read covariance by range from METAL-format files.
Read association statistics by gene from METAL-format files. Both scor...
Read association statistics by range from METAL-format files. Both sco...
Read null model statistics
Read score test statistics by range from METAL-format files.
Read skew by range from METAL-format files.
Write covariance association statistics files.
Write score-based association statistics files.
Efficiently Read Sequencing Data (VCF format, METAL format) into R
Read from binary PLINK file and return a genotype matrix
Create tabix index for bgzipped MetaScore/MetaCov file
Create tabix index file, similar to running tabix in command line.
Create tabix index for bgzipped VCF file
Read tabix file, similar to running tabix in command line.
Read tabix file, similar to running tabix in command line.
Read tabix file, similar to running tabix in command line.
Validate annotate parameter is valid
validate the inVcf can be created, and outVcf can be write to. will st...
Export workflow to Makefile
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.