The results of IBD probability calculations can be stored to and
loaded from plain text, tab-delimited .txt or .ibd
files using the functions
readIBDs. An IBD file should contain a header line, with
the first and second header named Marker and Genotype
to indicate the marker names and genotype names columns. The remaining
headers should contain the parent names to indicate the columns holding
the parent IBD probabilities. Each row in the file should hold the IBD
probabilities of the corresponding marker and genotype. I.e., the
probability that marker ‘x’ of genotype ‘y’ descends from parent
An example of the contents of a file with IBD probabilities is shown in the table below:
Note that for large data sets, this file can become very large. It is
therefore recommended to store this file in a compressed file format.
This can be done directly setting
compress = TRUE in
After having computed IBD probabilities, the results can be written
to a .txt or .ibd file using
## Compute IBD probabilities for Steptoe Morex. <- calcIBD(popType = "DH", SxMIBD markerFile = system.file("extdata/SxM", "SxM_geno.txt", package = "statgenIBD"), mapFile = system.file("extdata/SxM", "SxM_map.txt", package = "statgenIBD")) ## Write IBDs to tab-delimited .txt file. writeIBDs(SxMIBD, "SxM-IBD.txt")
The created file will look like as follows:
When writing the probabilities to a file it is possible to set the
maximum number of decimals written for the probabilities using the
decimals argument. By default 6 decimals are written to the
output. Trailing zeros are always removed. Values lower than a threshold
minProb can be set to 0.
## Write IBDs to file, set values <0.05 to zero and only print 3 decimals. writeIBDs(IBDprob = SxMIBD, outFile = tempfile(fileext = ".txt"), decimals = 3, minProb = 0.05)
Retrieving the IBD probabilities later on can be done using
readIBDs. This requires the not only the file with IBD
probabilities, but also the corresponding map file as a
data.frame. In this example we can use the map from the
SxMIBD object constructed earlier.
## Get map. <- SxMIBD$map SxMMap ## Read IBDs to tab-delimited .txt file. <- readIBDs("SxM-IBD.txt", map = SxMMap) SxMIBD summary(SxMIBD) #> population type: undefined #> Number of evaluation points: 116 #> Number of individuals: 150 #> Parents: Morex Steptoe
When reading the probabilities all values read are rescaled in such a way that the sum of the probabilities for each genotype x marker combination is equal to 1.