subPhased

This function takes a phased Beagle output and rewrites the output.

methods

Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.

Daniel Fischer

hoardeR

Collect and Retrieve Annotation Data for Various Genomic Data
Using Different Webservices

Anu Sironen

subPhased function

<dl> <dt>file</dt>
<dd>Location of the original Beagle file (<code>String</code>).</dd> <dt>vmmk</dt>
<dd>Location of the Variant Map Master key (<code>String</code>).</dd> <dt>out</dt>
<dd>Name and location of the output file (<code>String</code>).</dd> <dt>chunkSize</dt>
<dd>For large Beagle files, the chunk size.</dd> <dt>verbose</dt>
<dd>The function gives feedback.</dd> <dt>removeInsertions</dt>
<dd>All Indels will be removed.</dd></dl>

Arguments

Author

Rewrite the Phased File from a Beagle Output — subPhased

<dl>

 <dt>file</dt>
<dd>Location of the original Beagle file (<code>String</code>).</dd>

 <dt>vmmk</dt>
<dd>Location of the Variant Map Master key (<code>String</code>).</dd>

 <dt>out</dt>
<dd>Name and location of the output file (<code>String</code>).</dd>

 <dt>chunkSize</dt>
<dd>For large Beagle files, the chunk size.</dd>

 <dt>verbose</dt>
<dd>The function gives feedback.</dd>

 <dt>removeInsertions</dt>
<dd>All Indels will be removed.</dd>

</dl>

subPhased: Rewrite the Phased File from a Beagle Output

Description

Usage

Value

Arguments

Author

Details