setSummary | R Documentation |
This function is uses to ouput all the summary files after the creation of the atlas by the following two functions : 'makeAtlasByHotspots' and 'makeAtlasByDistance' is over.
setSummary( atlas, list.id, probs = TRUE, recap.by.segments = FALSE, q = 1e-04, HBD.threshold = 0.5, quality = 95, n.consecutive.markers = 5, phen.code = c("plink", "R") )
atlas |
a atlas object |
list.id |
you can either : - ignore this parameter if you want to compute HBD, FLOD and HFLOD for individuals who are considerated inbred and with a quality greater or equal to 95 - enter a list of individual for a computation of HBD, FLOD score HFLOD score for them - use "all" for a computation of HBD, FLOD score and HFLOD score for every individual |
probs |
a flag indicating if the HBD probabilities and FLOD score has been computed for the submaps (default is TRUE) |
recap.by.segments |
if the summary files has to be computed considering segments or snps (defaut is FALSE) (more information in the documentation of 'makeAtlasByHotspots' or'makeAtlasByDistance' functions) |
q |
Allows the user to choose the assumed frequency of the mutation involved in the disease for each individual (default is 0.0001) |
HBD.threshold |
value of the HBD probability threshold used to determine whether a segment is HBD or not (default is 0.5) |
quality |
The minimum percentage use to assume if a submap is valid (default is 95) |
n.consecutive.markers |
the number of consecutive markers with a probability equal or greater to the value of the threshold, to be used to find HBDsegments (default is 5) |
the function add content to the atlas object.
- summary for likelihood0/likelihood1
- summary for estimation of a and f
- summary for the submaps
- summary for HBD probabilities
- summary for HFLOD
- comutation of HBDsegments
return an atlas containing every summary created
Fantasio
makeAtlasByDistance
segmentsListByHotspots
festim
setHBDProbAndFLOD
setHBDProbAndFLODBySnps
setHFLOD
submapLikelihood
submapEstim
submapSummary
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