suggest_lod: Suggests a LOD Score for two point tests
In onemap: Construction of Genetic Maps in Experimental Crosses
suggest_lod R Documentation
Suggests a LOD Score for two point tests
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
suggest_lod(x)
Arguments
x
an object of class sequence or 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
Examples
data(onemap_example_bc) # Loads a fake backcross dataset installed with onemap
suggest_lod(onemap_example_bc) # An value that should be used to start the analysis
onemap documentation built on Nov. 26, 2022, 9:05 a.m.
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| suggest_lod | R Documentation |
Suggests a LOD Score for two point tests
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
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
Examples
data(onemap_example_bc) # Loads a fake backcross dataset installed with onemap suggest_lod(onemap_example_bc) # An value that should be used to start the analysis
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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