Description Usage Arguments Details Value Note Author(s) See Also Examples
One or several starting points for one or more genotype categories are estimated, given genotype data for a single marker
1 2 3 4 5 6 7 | getCenters(theta, gO = setGenoOptions(),
breaks = seq(-0.25, 1.25, gO$binWidth),
polyCent = generatePolyCenters(ploidy = gO$ploidy))
getSpecificCenters(theta, classification, gO = setGenoOptions(),
breaks = seq(-0.25, 1.25, gO$binWidth),
polyCent = generatePolyCenters(ploidy = gO$ploidy))
|
theta |
Numeric vector of “theta”-values for a marker, as given in
the |
gO |
List of genotype calling options. See |
breaks |
Histogram breakpoints. See |
polyCent |
List of all possible genotype categories with initial centre points
for the clustering. See |
classification |
Character string with a single genotype category |
Usually called from within other functions. The purpose of
getCenters
is to suggest a few of the most likely cluster
categories and corresponding starting points in ranked order. The
function getSpecificCenters
returns starting points for
a given genotype category
The function getCenters
returns a ranked list with elements
ix |
Numeric vector with index to categories returned from
|
centers |
List of initial centre points of clusters in “theta”-dimension |
The function getSpecificCenters
returns a numeric vector of
clustering starting values
For ploidy="tetra"
, the function has been empirically tuned to
find good starting point for each marker by calling
findClusters
repeatedly. Other ploidy has not been
implemented, but the function will return non-ranked genotype
categories with centre points corresponding to theoretical B allele
ratios. A warning will be issued to alert the user that the
suggested centre points are not optimized or ranked in any way
Lars Gidskehaug
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## Not run:
#Read pre-processed data directly into AlleleSetIllumina object
rPath <- system.file("extdata", package="beadarrayMSV")
normOpts <- setNormOptions()
dataFiles <- makeFilenames('testdata',normOpts,rPath)
beadFile <- paste(rPath,'beadData_testdata.txt',sep='/')
beadInfo <- read.table(beadFile,sep='\t',header=TRUE,as.is=TRUE)
BSRed <- createAlleleSetFromFiles(dataFiles[1:4],markers=1:10,beadInfo=beadInfo)
#Generate list of marker categories
gO <- setGenoOptions()
polyCent <- generatePolyCenters(ploidy=gO$ploidy)
print(polyCent)
#Suggest some candidate categories with initial centre points
ind <- 2
sConf <- getCenters(assayData(BSRed)$theta[ind,],gO=gO,polyCent=polyCent))
print(sConf)
print(polyCent$classification[sConf$ix])
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.