README

The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

pedFamilias

The purpose of pedFamilias is to facilitate data exchanging between the pedsuite packages and the Familias software. The main functions are readFam() and writeFam() for reading and writing .fam files associated with Familias. Notably, .fam files written with the DVI module of Familias are supported, and also database files without pedigree information.

These functions were originally part of forrel, but were split out to streamline maintenance and provide a more lightweight import for other packages otherwise independent of forrel.

Installation

install.packages("pedFamilias")

# install.packages("remotes")
remotes::install_github("magnusdv/pedFamilias")

Example

library(pedFamilias)

For a simple illustration of pedFamilias we read the example file paternity.fam shipped with the package:

fam = system.file("extdata", "paternity.fam", package = "pedFamilias")

peds = readFam(fam)
#> Familias version: 3.3.1 
#> Read DVI: No
#> 
#> Number of individuals (excluding 'extras'): 3 
#>   Individual 'AF': Genotypes for 10 markers read
#>   Individual 'MO': Genotypes for 0 markers read
#>   Individual 'CH': Genotypes for 10 markers read
#> 
#> Number of pedigrees: 2 
#>   Pedigree 'H1' (0 extra females, 0 extra males)
#>   Pedigree 'H2' (0 extra females, 0 extra males)
#> 
#> Database: unknown 
#> Number of loci: 10 
#>   D3S1358: 12 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   TH01: 10 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   D21S11: 26 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   D18S51: 23 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   PENTA_E: 21 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   D5S818: 9 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   D13S317: 9 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   D7S820: 19 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   D16S539: 9 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#>   CSF1PO: 11 alleles, mut model (M/F) = step-ext, rate = 0.002/0.001, range = 0.1, rate2 = 1e-06
#> 
#> Converting to `ped` format

plotPedList(peds, hatched = typedMembers, marker = 1)

Further analysis of the data may be carried out with the forrel package. For instance, the following command computes the likelihood ratio comparing the two hypotheses:

forrel::kinshipLR(peds)
#>    H1:H2    H2:H2 
#> 760.3445   1.0000

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.