View source: R/makeAtlasByHotspots.r
makeAtlasByHotspots | R Documentation |
This function creates N submaps and allows the creation of summary files
makeAtlasByHotspots( bedmatrix, n = 100, segmentsList = segmentsListByHotspots(bedmatrix), n.cores = 1, epsilon = 0.001 )
bedmatrix |
a bed.matrix object |
n |
the number of submaps wanted(default is 100) |
segmentsList |
a list of segment for each chromosomes |
n.cores |
the number of cores to use if you want to compute submaps using parellelism (default is 1) |
epsilon |
genotype error rate (default is 0.001) |
This function is used to create submaps by randomly picking a marker in each segment in the list of segments given by the argument segmentsList.
After the creation of one submap is finished, the function pass it to 'festim', a function that will computes different values (a, f, p.lrt, likelihood0, likelihood1)
After that we then creates the different summary to interpret easily the results of the computation.
This is done by the function 'setSummary'. This function will call all of the function neccessary to obtained the different summary needed for our data.
You can check all the summary after they are been created by accesing their slots.
When using recap.by.segments with true value, we then consider that the snps picked randomly in a segment is a representant of that segment.
When doing a number N of submaps using the options recap.by.segments,
the different values computed from the
snps picked randomly (a, f, p.lrt, ...) in a segments is considered different values
for the same segments.
return a new list object containing every dataframe and object created
Fantasio
makeAtlasByDistance
segmentsListByHotspots
festim
setHBDProb
setFLOD
setHFLOD
recap
setSummary
submapLikelihood
submapEstim
submapSummary
HBDSegments
#Please refer to vignette
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.