I use convert.snp.ped from GenABEL packages to converts genotypic data to use its in logistic regression in R I have PED file that look like

0   Tri1    0   0   0   0   00  00  00  00  00
0   Tri2    0   0   0   0   AA  00  00  00  00
0   Tri3    0   0   0   0   AA  AA  AA  AA  AA
0   Tri4    0   0   0   0   AA  AA  AA  AA  AA
0   Tri5    0   0   0   0   AA  AA  AA  AA  AA
0   Tri6    0   0   0   0   00  00  00  00  00
0   Tri7    0   0   0   0   AA  AA  AA  AA  AA
0   Tri8    0   0   0   0   AA  AA  AA  AA  AA
0   Tri9    0   0   0   0   AA  AA  AA  AA  AA
0   Tri10   0   0   0   0   00  00  00  00  00

And map file

0   rs72613040  0   0
0   rs377487780 0   0
0   rs374253281 0   0
0   rs72622300  0   0
0   rs368014648 0   0

Then i use convert. snp.ped function and as result i get outfile that looks like this

GenABEL raw data version 0.1

Tri1 Tri2 Tri3 Tri4 Tri5 Tri6 Tri7 Tri8 Tri9 Tri10 
rs72613040 rs377487780 rs374253281 rs72622300 rs368014648 
0 0 0 0 0 
0 0 0 0 0 
20 20 20 20 20 
00 00 00 00 00 
15 45 40 
05 45 40 
05 45 40 
05 45 40 
05 45 40

In that file i understand the first four lines, but what does the rest, I do not fully understand, and i am not sure that it's right i want get coded genotypes for all samples

Did somebody use the function convert.snp.ped ?

Tell me please what it should withdraw