pp.init | R Documentation |
Parameter initialization function for pushCross
and pullCross
pp.init(seg.thresh = 0.05, seg.ratio = NULL, miss.thresh = 0.1,
max.rf = 0.25, min.lod = 3)
seg.thresh |
Numerical value between zero and one determining the p-value threshold for the test of marker segregation distortion. |
seg.ratio |
A character string of the form "AA:BB" or "AA:AB:BB" describing the ratio of the alleles. |
miss.thresh |
Numerical value between zero and one determining the proportion of missing values. |
max.rf |
The maximum recombination fraction to consider when attempting to cluster pushed markers back into linkage groups. |
min.lod |
The minimum LOD score to consider when attempting to cluster pushed markers back into linkage groups. |
This parameter initialization function is used by the function pullCross
to
pull markers from a linkage map and pushCross
to push markers
back into a linkage map. How the arguments seg.thresh
,
seg.ratio
and miss.thresh
are used depends on which
function is called. See pushCross
and pullCross
for
more details.
Return user defined parameter values for each of the parameters.
Julian Taylor
Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.
pushCross
; pullCross
data(mapDH, package = "ASMap")
## pull markers from a linkage map with a segregation distortion
pars <- pp.init(seg.thresh = 0.05)
mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars = pars)
mapDH.s$seg.distortion$table
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.