Description Usage Arguments Value Author(s) Examples
Compares inferred ibd state with simulated "true" states. Calculates the proportion of markers called in the correct state, false positives (i.e. inferring ibd shared when none is shared), false negatives (i.e. inferring no ibd shared when ibd sharing is present) and the proportion of no calls.
1 | ibdhap.compare.loci(calls, true, data.type)
|
calls |
The data.frame created from running ibdhap.make.calls on ibd_haplo output. |
true |
The data frame of same dimension as calls, but with true (probably simulated) ibd states. |
data.type |
"h" : haplotypic data "g" : genotypic data (or hap data ran as genotypic) "r" : reduced data (output from running ibdhap.reduce.states and then ibdhap.make.states) |
Returns a list consisting of three matrices called "all", "ibd", "nonibd" and "categories".
The matrix for "all" contain a row for each of the following quantities, for all the loci:
Number of sites |
|
Called Correctly |
|
Called IBD Incorrectly |
|
Called noIBD Incorrectly |
The matrix for "ibd" contains a row for each of the following quantities, based on just the loci that are truly in an IBD state:
Number of sites |
|
Called Correctly |
|
Called as wrong IBD |
|
Called as no IBD |
|
No-call |
The matrix for "nonibd" contains a row for each of the follwing quantities, based on just the loci that are truly in an non-ibd state:
Number of sites |
|
Called Correctly |
|
Called as IBD |
|
No-call |
Finally, the matrix for "categories" tabulates the percentage of the loci that are truly in, and called to be in, each IBD state.
Fiona Grimson
1 2 3 4 5 6 7 8 9 10 11 | ## this example is taken from the package vignette.
##See vignette(IBDhaploRtools_tutorial)
data(qibd_phased)
data(ids_phased)
data(trueibd_phased)
phased.gold <- ibdhap.make.calls( qibd.file = qibd_phased,
ids.file= ids_phased, cutoff = 0.8)
ibdhap.compare.loci(phased.gold, trueibd_phased, "h")
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