gintervals.import_vcf

Reads a VCF/VCF.gz file and returns a misha 1D intervals data frame
with one row per record. VCF is 1-based; <code>start</code> is set to
<code>POS - 1</code> and <code>end</code> is set to <code>POS - 1 + nchar(REF)</code>,
yielding a 0-based half-open span covering the reference allele.

~import

~intervals

~VCF

A toolkit for analysis of genomic data. The 'misha' package
implements an efficient data structure for storing genomic data, and
provides a set of functions for data extraction, manipulation and
analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay
(2011) <doi:10.1038/ng.947>.

Aviezer Lifshitz

misha

Toolkit for Analysis of Genomic Data

Misha Hoichman

Eitan Yaffe

Amos Tanay

Weizmann Institute of Science 

gintervals.import_vcf function

<dl><dt>file</dt>
<dd>path to a VCF/VCF.gz file.</dd>
<dt>info</dt>
<dd>if <code>TRUE</code>, include the raw INFO column as
<code>info</code>. The string is not parsed.</dd></dl>

Arguments

Import intervals from a VCF file — gintervals.import_vcf

<dl>

<dt>file</dt>
<dd>path to a VCF/VCF.gz file.</dd>


<dt>info</dt>
<dd>if <code>TRUE</code>, include the raw INFO column as
<code>info</code>. The string is not parsed.</dd>

</dl>

gintervals.import_vcf: Import intervals from a VCF file

Description

Usage

Value

Arguments

Details

See Also