segregating: Identify segregating sites among a group of samples
In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays
Description
Usage
Arguments
Details
Value
See Also
Description
Identify segregating sites among a group of samples
Usage
1
segregating(gty, nas.allowed = 0, allow.het = TRUE, ...)
Arguments
gty
a genotypes object
nas.allowed
maximum proportion of missing genotypes to ignore
allow.het
logical; if FALSE, ignore samples with heterozygous genotype
...
ignored
Details
A site is defined to be "segregating" if two or more alleles are present in one or
more copies across all samples. Sites at which missingness is greater than nas.missing
are set to NA.
When allow.het = FALSE, this is equivalent to asking whether at least one pair of samples
has a fixed difference at each site.
Value
a named logical vector, of length equal to the number of rows in gty,
indicating whether a site is segregating
See Also
andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value See Also
Description
Identify segregating sites among a group of samples
Usage
1 | segregating(gty, nas.allowed = 0, allow.het = TRUE, ...)
|
Arguments
gty |
a |
nas.allowed |
maximum proportion of missing genotypes to ignore |
allow.het |
logical; if |
... |
ignored |
Details
A site is defined to be "segregating" if two or more alleles are present in one or
more copies across all samples. Sites at which missingness is greater than nas.missing
are set to NA.
When allow.het = FALSE, this is equivalent to asking whether at least one pair of samples
has a fixed difference at each site.
Value
a named logical vector, of length equal to the number of rows in gty,
indicating whether a site is segregating
See Also
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.