Users' documentation for rTDT in c++

Installation

Compiled version:

Compiled version for linux.-After you have succesfully obtained the archive you can execute the following Unix commands to install the program:

• gunzip rTDT1.0.gz
• chmod 755 rTDT.out

Source code version:

Source code version for linux.-After you have succesfully obtained the archive you can execute the following Unix commands to install the program:

• tar xvzf rTDT1.0.tar.gz
• make

Execution

To use rTDT, use the following command line:

./rTDT1.0 <filename> <#TotalSNPs> <#individuals>

where <filename> is the input file with format as shown below, <#TotalSNPs> the number of SNPs in the file and <#individuals> the number of individuals in the file.

Format of the input file

A text file of SNP data set, one row per individual, 7 + 2xTotalSNPs columns, with TotalSNPs being the number of SNPs. Columns must be separared by a blank or tab character.Each column must contain an integer. See an example of input file.

Description of columns:

• Column 1: family code
• Column 2: individual code
• Column 3: father code (0 if the individual is not a child)
• Column 4: mother code (0 if the individual is not a child)
• Column 5: gender (not used by rTDT)
• Column 6: affection status (not used by rTDT)
• Column 7: another individual id (not used by rTDT)
• Columns 8 until 7+2*TotalSNPs: SNPs values (each SNP uses two contiguous columns). Example: if SNP1 value for an individual is 12 (heterozygous), column8 will have the value 1 and column9 will have the 2.

Output for the function rTDT

Output will be written at a file with the same name that the input file name but with the extension ".sal". The output file is a text file with one column per SNP separated by blanks, so there will be TotalSNPs columns.
The file will have 12 rows:

Description of rows:

• Row 1: b (=m3+m6+2m8+m9)
• Row 2: c (=m4+m7+m9+2m10)
• Row 3: b1 (=b+n9)
• Row 4: c1 (=c+n11)
• Row 5: bmax (=b+2xn2+n3+n5+n6+2xn8+2xn9+n10+n12+n13+n15+2xn16+n17)
• Row 6: cmax (=c+n3+2xn4+n5+n7+2xn8+n10+2xn11+n12+n14+n15+2xn16+n17)
• Row 7: t (=T(b,c)) (standard TDT)
• Row 8: p value for t
• Row 9: tmin (if b1>cM then tmin=T(b1,cM) else if bM<c1 then tmin=T(bM,c1)
  else Tmin=0)
• Row 10: p value tmin
• Row 11: tmax=max(T(bM,c1),T(b1,cM))
• Row 12: p value tmax

References

Sebastiani, Paola; Abad, María; Alpargu, Gulhan; Ramoni, Marco
Robust Transmission/Disequilibrium Test for Incomplete Family Genotypes
Genetics, Vol 168, 2329-2337