Convert genotype data to Familias format


Genotype data are transformed from lines two columns. If there is only one column for each marker and two lines for each individual, the data is transformed so that there is one line for each individual. The pecularities of the input format of Familias is handled.


convertToFamilias(infile, outfile = paste("out", infile, sep = ""))



File name.


File name for output file.


The first column is the name of the individual, the second indicates sex (X X for females, X Y for males) while the remaining columns are marker names (no blanks are allowed in names; usual rules for variable names apply). There are two lines for each individual. The smallest example (below) is for a female called 32293 with genotypes 15/16 for Marker1:

Name Sex Marker
32293 X 15
32293 X 16

Typically, Familias is started by loading a file containing the database (markers and allele frequencies). This file needs only be prepared once for each individual. The Case Related DNA Data can then be read from the file produced by convertToFamilias. Note that allele must have precisely the same name (8 and 8.0 are different alleles for instance)


A file with default file name as input file name preceded by "out". This file can be read by Familias in the Case Related DNA Data window.



## Not run: convertToFamilias("denise3.txt") 

Want to suggest features or report bugs for Use the GitHub issue tracker. Vote for new features on Trello.

comments powered by Disqus