RealStudy {FEST}R Documentation

Analysis of alternative hypothesized family relations for observed marker data

Description

Based on observed marker data, likelihood and posterior values are computed for alternative hypothesized family relations.

Usage

RealStudy(altModels, dataPars, saveMerlinFiles, limitCentiMorgan=0,
          freqThreshold=0)

Arguments

altModels Vector of strings that gives alternative family relations. See SetModels for a list of the family relations that can be used.
dataPars List: Output from function SetDataPars
saveMerlinFiles If TRUE the files used as input to the likelihood computations in merlin are saved. Default value is FALSE.
limitCentiMorgan Markers are thinned such that the distance between two consecutive markers are larger than this limit.
freqThreshold Includes only markers with minor allele frequency larger than this threshold.

Value

logLiks log likelihood values
posterior posterior values

Author(s)

Øivind Skare oivind.skare@medisin.uio.no

References

http://folk.uio.no/thoree/FEST

Øivind Skare, Nuala Sheehan, and Thore Egeland Identification of distant family relationships Bioinformatics Advance Access published on July 6, 2009.

Examples

## The example can not be run, user must supply data
## Not run: pathDataDir <- "../Data/RealData/" ## path to data directory
## Not run: chrdirs <- paste("Chr", 1:22, sep="")
## Not run: 
dataPars <- SetDataPars(pathDataDir, chrdirs=chrdirs,
prefixInputFiles="", format="linkage", famList=32,
individualsTyped=rbind(c(32,33), c(31,33), c(30,33), c(26,33)))
## End(Not run)
## Not run: 
realObj <- RealStudy(altModels=c("S-1", "HS-1", "S-2", "S-3","unrelated"),
 dataPars)
## End(Not run)

## A simple test example: Two persons assumed to be half-sibs, 2 markers
## Make first data files (qtdt format)
ped <- rbind(c(1, 1, 0, 0, 2, 0, 0, 0, 0),
             c(1, 2, 0, 0, 1, 0, 0, 0, 0),
             c(1, 3, 0, 0, 2, 0, 0, 0, 0),
             c(1, 4, 2, 1, 1, 1, 2, 1, 1),
             c(1, 5, 2, 3, 1, 1, 1, 2, 2))
dat <- rbind("M  locus1", "M  locus2")
freq <- rbind("M locus1", "F 0.4 0.6", "M locus2", "F 0.7 0.3")
map <- rbind("CHROMOSOME MARKER POSITION",
             "1          locus1     123.4",
             "1          locus2     136.2")
write.table(ped, file="test1.ped", col.names=FALSE, row.names=FALSE)
write.table(dat, file="test1.dat", col.names=FALSE, row.names=FALSE, quote=FALSE)
write.table(freq, file="test1.freq", col.names=FALSE, row.names=FALSE, quote=FALSE)
write.table(map, file="test1.map", col.names=FALSE, row.names=FALSE, quote=FALSE)

## Analysis of this data set
mypath <- "."
chrdirs <- NULL
suffixPed <- ".ped"
format <- "qtdt"
famList <- 1
individualsTyped <- cbind(4,5)
prefixInputFiles <- "test1"
dataPars <- SetDataPars(path=mypath, chrdirs=chrdirs,
                        suffixPed=suffixPed,
                        prefixInputFiles=prefixInputFiles, format=format,
                        famList=famList, individualsTyped=individualsTyped)
realObj <- RealStudy(altModels=c("HS-1", "HS-2", "HS-3",
                                 "S-1", "unrelated"), dataPars)
## realObj$posterior
##         HS-1      HS-2      HS-3        S-1 unrelated
##4-5 0.1440720 0.2432792 0.2669072 0.07134156 0.2743999

## Take away the second locus and compare three family relations that
## should give equal likelihood for 1 marker (and more generally for
## unlinked markers)

dat <- rbind("M  locus1", "S2  locus2") # S2: skips the locus
write.table(dat, file="test1.dat", col.names=FALSE, row.names=FALSE, quote=FALSE)
realObj <- RealStudy(altModels=c("HS-1", "S-1-2", "PC-2",
                                 "unrelated"), dataPars)
## realObj$logLiks
##        HS-1     S-1-2      PC-2 unrelated
##4-5 -2.448768 -2.448768 -2.448768 -2.566551
## realObj$posterior
##         HS-1     S-1-2      PC-2 unrelated
##4-5 0.2571429 0.2571429 0.2571429 0.2285714

[Package FEST version 0.06 Index]