get.sig.thr: Given a set of maximum LOD scores, calculate the significance...
In elijahedmondson/HZE: Mapping suscetibility loci in HZE irradiated HS/npt mice
Description
Given a set of maximum LOD scores, calculate the significance thresholds
for the given levels. Note that we use the method of Broman et.al., Genetics,
2006 to calculate the X chromosoem threshold.
Daniel Gatti
dan.gatti@jax.org
Oct. 26, 2015
Arguments: perms: either a vector with the maximum LOD score from permutations
or, if Xchr == TRUE, a matrix with colnames 'A' and 'X'
containing the maximumum autosomal and X chr LOD scores from
permutations.
alpha: numeric vector, one or more numerical value that are the
alpha levels of the significane thresholds.
Xchr: logical indicating whether the X chromosome should have
a separate threshold. If TRUE, then perms must be a matrix
with 2 named columns as described above.
NOTE: If using p-values, don't forget to take -log10(p.value) of the
permuations before calling this function.
Usage
1
get.sig.thr(perms, alpha = 0.05, Xchr = TRUE)
elijahedmondson/HZE documentation built on May 16, 2019, 3 a.m.
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Description
Given a set of maximum LOD scores, calculate the significance thresholds for the given levels. Note that we use the method of Broman et.al., Genetics, 2006 to calculate the X chromosoem threshold. Daniel Gatti dan.gatti@jax.org Oct. 26, 2015 Arguments: perms: either a vector with the maximum LOD score from permutations or, if Xchr == TRUE, a matrix with colnames 'A' and 'X' containing the maximumum autosomal and X chr LOD scores from permutations. alpha: numeric vector, one or more numerical value that are the alpha levels of the significane thresholds. Xchr: logical indicating whether the X chromosome should have a separate threshold. If TRUE, then perms must be a matrix with 2 named columns as described above. NOTE: If using p-values, don't forget to take -log10(p.value) of the permuations before calling this function.
Usage
1 | get.sig.thr(perms, alpha = 0.05, Xchr = TRUE)
|
R Package Documentation
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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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