View source: R/linkage.power.R
linkage.power | R Documentation |
Power analysis of parametric linkage studies
linkage.power( x, N = 100, available = x$available, afreq = c(0.5, 0.5), loop_breakers = NULL, threshold = NULL, seed = NULL, verbose = FALSE ) ## S3 method for class 'powres' summary(object, threshold = NULL, ...)
x |
a |
N |
an integer; the number of markers to simulate. |
available |
a vector containing IDs of the available individuals, i.e. those whose genotypes should be simulated. |
afreq |
a numerical vector with sum 1; the population frequencies for the marker alleles. |
loop_breakers |
a numeric containing IDs of individuals to be used as
loop breakers. Relevant only if the pedigree has loops. See
|
threshold |
NULL, or a single numeric. If numeric, the output includes
the percentage of simulated markers having LOD larger than
|
seed |
NULL, or a numeric seed for the random number generator. |
verbose |
a logical passed on to |
object |
a |
... |
not used. |
The function prints a summary and returns invisibly a powres
object, which is a list with the following entries:
sim |
A
|
lod |
The LOD scores (computed with recombination fraction theta=0) of the simulated markers |
maxlod |
The highest LOD score of the simulated markers |
elod |
The average LOD score for the simulated markers |
returns the maximum LOD score for each element of values
.
Marker simulation is inspired by the SLINK algorithm: https://www.jurgott.org/linkage/SLINK.htm.
linkdat
, linkageSim
# Note: In the examples below N is set very low in order to reduce time consumption. # Increase N to get more interesting results. x = nuclearPed(3) x = swapAff(x, c(1,3,4)) x = setModel(x, 1) # Autosomal dominant linkage.power(x, N=1) # X-linked recessive example: y = linkdat(Xped, model=4) linkage.power(y, N=1) # Power of homozygosity mapping: z = addOffspring(cousinPed(1), father=7, mother=8, noffs=1, aff=2) z = setModel(z, 2) # Autosomal recessive model pow = linkage.power(z, N=1, loop_breaker=7, seed=123) stopifnot(round(pow$maxlod, 1) == 1.2)
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