readVCFToMatrixByRange

Read a gene from VCF file and return a genotype matrix

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.

Xiaowei Zhan

seqminer

Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R

Dajiang Liu

Attractive Chaos 

Broad Institute / Massachusetts Institute of Technology 

Genome Research Ltd (GRL) 

Facebook, Inc 

D. Richard Hipp 

readVCFToMatrixByRange function

<dl><dt>fileName</dt>
<dd>character, represents an input VCF file (Bgzipped, with Tabix index)</dd>
<dt>range</dt>
<dd>character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index</dd>
<dt>annoType</dt>
<dd>character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty.</dd></dl>

Arguments

Read a gene from VCF file and return a genotype matrix — readVCFToMatrixByRange

<dl>

<dt>fileName</dt>
<dd>character, represents an input VCF file (Bgzipped, with Tabix index)</dd>


<dt>range</dt>
<dd>character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index</dd>


<dt>annoType</dt>
<dd>character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty.</dd>

</dl>

readVCFToMatrixByRange: Read a gene from VCF file and return a genotype matrix

Description

Usage

Value

Arguments

See Also

Examples