is_loci_table_ordered

is_loci_table_ordered.tbl_df

is_loci_table_ordered.vctrs_bigSNP

This functions checks that all SNPs in a chromosome are adjacent in the loci
table, and that positions are sorted within chromosomes.

We provide a tidy grammar of population genetics, facilitating
the manipulation and analysis of data on biallelic single nucleotide
polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets
by storing genotypes on disk, and performing operations on them in
chunks, without ever loading all data in memory. The full
functionalities of the package are described in Carter et al. (2025)
<doi:10.1111/2041-210x.70204>.

Andrea Manica

tidypopgen

Tidy Population Genetics

Evie Carter

Eirlys Tysall

Chang Christopher

Shaun Purcell

Bengtsson Henrik

is_loci_table_ordered function

<dl><dt>.x</dt>
<dd>a vector of class <code>vctrs_bigSNP</code> (usually the <code>genotype</code> column of
a <code>gen_tibble</code> object), or a <code>gen_tibble</code>.</dd>
<dt>error_on_false</dt>
<dd>logical, if <code>TRUE</code> an error is thrown if the loci are
not ordered.</dd>
<dt>ignore_genetic_dist</dt>
<dd>logical, if <code>TRUE</code> the physical position is not
checked.</dd>
<dt>...</dt>
<dd>other arguments passed to specific methods.</dd></dl>

Arguments

Test if the loci table is ordered — is_loci_table_ordered

<dl>

<dt>.x</dt>
<dd>a vector of class <code>vctrs_bigSNP</code> (usually the <code>genotype</code> column of
a <code>gen_tibble</code> object), or a <code>gen_tibble</code>.</dd>


<dt>error_on_false</dt>
<dd>logical, if <code>TRUE</code> an error is thrown if the loci are
not ordered.</dd>


<dt>ignore_genetic_dist</dt>
<dd>logical, if <code>TRUE</code> the physical position is not
checked.</dd>


<dt>...</dt>
<dd>other arguments passed to specific methods.</dd>

</dl>

is_loci_table_ordered: Test if the loci table is ordered

Description

Usage

Value

Arguments

Examples