IBD probabilities file format

File format

The results of IBD probability calculations can be stored to and loaded from plain text, tab-delimited .txt or .ibd files using the functions writeIBDs and 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 ‘z’.

An example of the contents of a file with IBD probabilities is shown in the table below:

Marker Genotype Parent1 Parent2 … ParentN
M001 G001 0.5 0.5 … 0
M001 G002 0 1 … 0
M001 G003 0 0.5 … 0.5
… … … … … …
M002 G001 0 0.5 … 0.5
M002 G002 0.25 0.75 … 0
… … … … … …

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 writeIBDs.

Examples

Writing IBD probabilities to a file

After having computed IBD probabilities, the results can be written to a .txt or .ibd file using writeIBDs.

## Compute IBD probabilities for Steptoe Morex.
SxMIBD <- calcIBD(popType = "DH",
                  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:

Marker Genotype Morex Steptoe
plc dh001 0 1
plc dh002 0 1
plc dh003 0 1
plc dh004 0 1
plc dh005 0 1
plc dh006 0 1

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 specified by 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)

Reading IBD probabilities from file

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.
SxMMap <- SxMIBD$map

## Read IBDs to tab-delimited .txt file.
SxMIBD <- readIBDs("SxM-IBD.txt", map = SxMMap)
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.