get_site_dist: Determine whether a variant site is fixed or polymorphic
In surh/HMVAR: Human Microbiome Variant Analysis in R
Description
Usage
Arguments
Details
Value
Description
This is an internal utility function
Usage
1
get_site_dist(d, group_thres = 2)
Arguments
d
A data table that matches each site at each
sample with the group of that sample. Must have column
'allele' which must have two values only; column 'Group'
which is the grouping factor (can be character) with two
levels.
group_thres
The minimum number of samples per
group to consider the site.
Details
Looks at the distribution of alleles at one site and
determines how it distributes with respect to a grouping factor.
If the site perfectly separates both groups it is 'Fixed'
and 'Polymorphic' otherwise.
Assumes grouping factor with two levels (NO CHECKS!!)
Assumes bi-allelic site indicated by character string (NO CHECKS!!)
Assumes only data from one site is give (NO CHECKS!!)
USE WITH CARE!!
Value
A character string indicating the type of site:
'Fixed', 'Polymorphic', 'Invariant' or NA.
surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.
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Description Usage Arguments Details Value
Description
This is an internal utility function
Usage
1 | get_site_dist(d, group_thres = 2)
|
Arguments
d |
A data table that matches each site at each sample with the group of that sample. Must have column 'allele' which must have two values only; column 'Group' which is the grouping factor (can be character) with two levels. |
group_thres |
The minimum number of samples per group to consider the site. |
Details
Looks at the distribution of alleles at one site and determines how it distributes with respect to a grouping factor. If the site perfectly separates both groups it is 'Fixed' and 'Polymorphic' otherwise.
Assumes grouping factor with two levels (NO CHECKS!!)
Assumes bi-allelic site indicated by character string (NO CHECKS!!)
Assumes only data from one site is give (NO CHECKS!!)
USE WITH CARE!!
Value
A character string indicating the type of site: 'Fixed', 'Polymorphic', 'Invariant' or NA.
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.
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