snp_modifyBuild

Modify the physical position information of a data frame
when converting genome build using executable liftOver.

Easy-to-use, efficient, flexible and scalable tools for analyzing
massive SNP arrays. Privé et al. (2018) <doi:10.1093/bioinformatics/bty185>.

Florian Privé

bigsnpr

Analysis of Massive SNP Arrays

Michael Blum

Hugues Aschard

Bjarni Jóhann Vilhjálmsson

snp_modifyBuild function

<dl><dt>info_snp</dt>
<dd>A data frame with columns "chr" and "pos".</dd>
<dt>liftOver</dt>
<dd>Path to liftOver executable. Binaries can be downloaded at
<a href="https://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftOver">https://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftOver</a> for Mac
and at <a href="https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver">https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver</a>
for Linux.</dd>
<dt>from</dt>
<dd>Genome build to convert from. Default is <code>hg18</code>.</dd>
<dt>to</dt>
<dd>Genome build to convert to. Default is <code>hg19</code>.</dd></dl>

Arguments

Modify genome build — snp_modifyBuild

<dl>

<dt>info_snp</dt>
<dd>A data frame with columns "chr" and "pos".</dd>


<dt>liftOver</dt>
<dd>Path to liftOver executable. Binaries can be downloaded at
<a href='https://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftOver'>https://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/liftOver</a> for Mac
and at <a href='https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver'>https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver</a>
for Linux.</dd>


<dt>from</dt>
<dd>Genome build to convert from. Default is <code>hg18</code>.</dd>


<dt>to</dt>
<dd>Genome build to convert to. Default is <code>hg19</code>.</dd>

</dl>

snp_modifyBuild: Modify genome build

Description

Usage

Value

Arguments

References