How prepare input from ped file with genotyping data #4
Description
Dear Torsten
I am very interested HaploBlocker tool to perform haplotype block analysis of my data. Haploview with Gabriel method gave nothing special so I thought that may your algorythm would be more helpful here. However, I think I have problem with correct input format. Please note, that I am not advanced bioinformatic user and I am still learning this ;)
I have genotyping data of 190 human samples for 17 SNPs from one gene in standard plink format so there is ped file. Each of these SNPs has two alleles so each samples has 34 alleles and it looks like this (first six columns in ped are informations and I bolded them, columns are separated by tab, and alleles of the same SNP by space):
22 subject-22 0 0 0 1 3 3 1 1 1 1 2 2 2 1 1 1 2 2 2 2 4 4 3 3 3 3 3 3 1 1 1 1 3 3 4 2 1 1
When I tried to perform block_calculation function I see:
Error in command 'fixcoding(unique.dhm)':
maximum number of 'values' is 256. Got 395.
I saw in instruction that standard input is haplotypes dataset, however I have ped file with doubled alleles. On the other hand, in your publication you presented results of analysis of huge datasets so this is somehow possible but I do not know for such the data as mine. Could you explain how can I perform correctly input file to HaploBlocker from my dataset, if it is possible at all, for such the data?
Thank you in advance, I will be very glad :)
Marcin Słomka