Segregation probability
Format
There are four lines per individual, corresponding to the four possible patterns of segregation (inheritance):
The grand paternal allele from the father and the grand paternal allele from the mother: \(Pr(F_{p,-} \& M_{p,-})\),
The grand paternal allele from the father and the grand maternal allele from the mother: \(Pr(F_{p,-} \& M_{-,m})\),
The grand maternal allele from the father and the grand paternal allele from the mother: \(Pr(F_{-,m} \& M_{p,-})\), and
The grand maternal allele from the father and the grand maternal allele from the mother: \(Pr(F_{-,m} \& M_{-,m})\).
The symbols above mean the following:
Pr() probability,
F father,
M mother,
p paternal allele,
m maternal allele, and
- the allele that was not inherited.
The first value in each line is the individual ID. The remaining values are segregation probabilities at each locus.
Example with four individuals and four loci:
id1 0.2500 0.2500 0.2500 0.2500
id1 0.2500 0.2500 0.2500 0.2500
id1 0.2500 0.2500 0.2500 0.2500
id1 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id3 0.3356 0.3894 0.5000 0.4390
id3 0.1644 0.1106 0.0000 0.0610
id3 0.3356 0.3894 0.5000 0.4390
id3 0.1644 0.1106 0.0000 0.0610
id4 0.2046 0.1953 0.2760 0.3914
id4 0.2954 0.3047 0.2240 0.1086
id4 0.2046 0.1953 0.2760 0.3914
id4 0.2954 0.3047 0.2240 0.1086
Input details
This input file is obtained from the output of the multi-peeling cycle of the hybrid peeling,
and is only required and allowed for the single-peeling cycle of the hybrid peeling.
If provided, values from this file initializes the segregation probabilities in the current analysis.
See details of segregationTensor in function explanation for more explanation of
how segregation probabilities are used in the peeling cycle.
Output details
The file is saved as .seg_prob.txt.
The file contains all individuals from all inputs.