suggest.lod: Suggests a LOD Score for two point tests
In BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species
Description
Usage
Arguments
Details
Value
Description
It suggests a LOD Score for declaring statistical significance for two-point tests
for linkage between all pairs of markers, considering that multiple tests are being performed.
Usage
1
suggest.lod(x)
Arguments
x
an object of class onemap
Details
In a somehow naive approach, the function calculates the number of two-point tests that
will be performed for all markers in the data set, and then using this to calculate
the global alpha required to control type I error using Bonferroni's correction.
From this global alpha, the corresponding quantile from the chi-square distribution is taken
and then converted to LOD Score.
This can be seen as just an initial approximation to help users to select a LOD Score for two
point tests.
Value
the suggested LOD to be used for testing linkage
BatchMap documentation built on May 2, 2019, 3:45 p.m.
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Description Usage Arguments Details Value
Description
It suggests a LOD Score for declaring statistical significance for two-point tests for linkage between all pairs of markers, considering that multiple tests are being performed.
Usage
1 | suggest.lod(x)
|
Arguments
x |
an object of class |
Details
In a somehow naive approach, the function calculates the number of two-point tests that will be performed for all markers in the data set, and then using this to calculate the global alpha required to control type I error using Bonferroni's correction.
From this global alpha, the corresponding quantile from the chi-square distribution is taken and then converted to LOD Score.
This can be seen as just an initial approximation to help users to select a LOD Score for two point tests.
Value
the suggested LOD to be used for testing linkage
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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