Users' documentation for rTDT in Matlab
Overview
The archive rTDT contains
the following M-files:
- rTDT
- EnesTrios
- EmesTrios
- IsAChild
- NonMissingSNP
- IsHetero
- IsHomo1
- IsHomo2
- GetMajorAllele
- Father
- Mother
The main function rTDT needs
as an only argument a table with SNPs values. The rTDT function returns a table
with Chi-Square for TDT and rTDT, p values and all the quantities needed
to compute these values.
Input for the function
rTDT
SNP dataset, one row per
individual, 7 + 2xTotalSNPs columns, with TotalSNPs being the
number of SNPs. Each column must contain an integer.
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)
- Column 6: affection status
(not used)
- Column 7: another individual
id (not used)
- 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
Table
robustTDT, with one column per SNP, then there will be TotalSNPs
columns.
The table has 45 rows.
Description of rows:
- Rows 1 to 21: n1, n2, ..., n21
- Rows 22 to 31: m1, m2,
m3, ..., m10
- Row 32: b (=m3+m6+2m8+m9)
- Row 33: c (=m4+m7+m9+2m10)
- Row 34: b1 (=b+n9)
- Row 35: c1 (=c+n11)
- Row 36: bmax (=b+2xn2+n3+n5+n6+2xn8+2xn9+n10+n12+n13+n15+2xn16+n17)
- Row 37: cmax (=c+n3+2xn4+n5+n7+2xn8+n10+2xn11+n12+n14+n15+2xn16+n17)
- Row 38: T(b,c) (standard
TDT)
- Row 39: T(bM,c1)
- Row 40: T (b1,cM)
- Row 41: Tmin (if b1>cM
then Tmin=T(b1,cM) else if bM<c1 then Tmin=T(bM,c1)
else Tmin=0)
- Row 42: Tmax=max(T(bM,c1),T(b1,cM))
- Row 43: pvalue T
- Row 44: pvalue Tmin
- Row 45: pvalue Tmax
References
Sebastiani, Paola; Abad, María; Alpargu, Gulhan; Ramoni, Marco
Robust Transmission/Disequilibrium Test for Incomplete Family Genotypes
Genetics, Vol 168, 2329-2337