[.PlinkFile

Read from binary PLINK 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 

[.PlinkFile function

<dl><dt>plinkFileObject</dt>
<dd>a PlinkFileObject obtained by openPlink()</dd>
<dt>sampleIndex</dt>
<dd>integer, 1-basd, index of samples to be extracted</dd>
<dt>markerIndex</dt>
<dd>integer, 1-basd, index of markers to be extracted</dd></dl>

Arguments

Read from binary PLINK file and return a genotype matrix — [.PlinkFile

<dl>

<dt>plinkFileObject</dt>
<dd>a PlinkFileObject obtained by openPlink()</dd>


<dt>sampleIndex</dt>
<dd>integer, 1-basd, index of samples to be extracted</dd>


<dt>markerIndex</dt>
<dd>integer, 1-basd, index of markers to be extracted</dd>

</dl>

[.PlinkFile: Read from binary PLINK file and return a genotype matrix

Description

Usage

Value

Arguments

See Also

Examples