manualCall: Interactive calling of genotype for single marker
In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Description Usage Arguments Details Value Author(s) See Also Examples

Function usually called from within callGenotypes.interactive, in order to define clusters by clicking and dragging with the mouse

1	manualCall(marker, cntIdeal, classification, gg = NULL, close.gg = TRUE)

`marker`	Data-frame containing the columns “Theta”, “R”, and optionally “PedCheck” and “PedigreeID” for a single marker. The first two correspond to `assayData` entries “theta” and “intensity” of an `"AlleleSetIllumina"` object. The “PedCheck” column corresponds to the output from `validateSingleCall`. The “PedigreeID” consists of strings <p><mmm><fff><oo>, where “p”, “mmm”, “fff”, and “oo” are unique identifiers for population, mother, father, and individual within full-sib group, respectively. “000” means founding parent, whereas “999” means unknown parent. May also include a vector of B allele ratios “Call” with results from a previous clustering, in which case this is used as starting values
`cntIdeal`	A numeric vector of the allowed B allele ratios for a specific genotype category (see `generatePolyCenters`)
`classification`	Character string denoting genotype category (see `generatePolyCenters`)
`gg`	An instance of `"ggobi"`
`close.gg`	If `TRUE`, an updated data-frame `marker` is returned and `gg` is closed. Otherwise, `gg` is returned directly

A “GGobi” interactive scatter-plot is produced. Round dots with colours purple, pink, red, blue, green and grey denote samples of “Theta” values 0, 1/4, 1/2, 3/4, 1, and NA, respectively. Orange and brown square dots indicate offspring and parent pedigree errors, respectively. Select (“brush”) points by moving around the yellow rectangle visible on the screen using the left mouse button. Change the shape of the rectangle using the right mouse button.

If pedigree errors are found after clustering, a warning is issued, and the user is given the choice between un-assigning erroneous offspring, modifying the clusters, or disregarding the errors. Note that by setting erroneous samples to missing, the remaining calls may appear better than they are.

Depending on the value of close.gg, a data-frame or an object of class "ggobi" is returned, containing marker data including a column “Call” with the B allele ratio for each subject

Lars Gidskehaug

ggobi, callGenotypes.interactive

## Not run: 
#Read 10 markers into an 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)

#Prepare a single marker
ind <- 2
marker <- data.frame(Theta=assayData(BSRed)$theta[ind,],
    R=assayData(BSRed)$intensity[ind,],
    PedigreeID=pData(BSRed)$PedigreeID,
    stringsAsFactors=FALSE)

#Cluster marker from scratch, assuming MSV-5
polyCent <- generatePolyCenters(ploidy="tetra")
iMSV5 <- 7
marker1 <- manualCall(marker,cntIdeal=polyCent$centers[[iMSV5]],
    classification=polyCent$classification[[iMSV5]],close.gg=FALSE)

## End(Not run)