1. Prepare data for Microdeletion
Jianfang Chen

2. 1. Original Data Set.

3. (1) snp_homozygosity_data. (2) snp_location_data. (3) Parameter file.
2. Objective Data Sets.
(1) snp_homozygosity_data.
(2) snp_location_data.
(3) Parameter file.

4. snp_homozygosity_data -- The first row is the title line
snp_homozygosity_data -- The first row is the title line. The first column is affection_status (0 for controls, 1 for cases). The remaining columns are homozygosity data at each site ( 0 for missing, 1 for homozygotes, 2 for heterozygotes).
Example of "snp_homozygosity_data" (with two controls, two cases, 6 SNPs):
indicator v1 v2 v3 v4 v5 v6

5. snp_location_data -- The first row is the title line
snp_location_data -- The first row is the title line. The first column is SNP index number. Second col is SNP location. The locations are sorted in increasing order.
Example of "snp_location_data" (with 6 SNPs):
order position

6. Parameter file -- It needs the following inputs (one input per line):
snp_homozygosity_data_name,
snp_location_data_name,
output_file_name,
num_cont,
num_case,
num_site,
maximum_window_size,
num_rep1

7. 3. Algorithm sort orginal data by FamilyID, Position and Marker_name.
remove one marker with duplicate position.
for each family within a marker (3 individuals)
leave child as case

8. combine father and mother into one line as control, based on the following algorithm:
suppose father (a,b) mother (c,d) and child (e,f)
if e=a and f=c then control will be (b,d)
else if e=a and f=d then control will be (b,c)
else if e=b and f=c then control will be (a,d)
else if e=b and f=d then control will be (a,c)
else if e=c and f=a then control will be (d,b)
else if e=c and f=b then control will be (d,a)
else if e=d and f=a then control will be (c,b)
else if e=d and f=b then control will be (c,a)

9. else if a=1 and b=1 and c=1 and d=1 and e=2 and f=2 then control will be (1,1) else if a=2 and b=2 and c=2 and d=2 and e=1 and f=1 then control will be (2,2) else if a=1 and b=1 and c=1 and d=1 and e=2 and f=2 then control will be (1,1) else if a=2 and b=2 and c=2 and d=2 and e=1 and f=1 then control will be (2,2) else if a=1 and b=1 and c=2 and d=2 and e=1 and f=1 then control will be (1,2) else if a=2 and b=2 and c=1 and d=1 and e=1 and f=1 then control will be (1,2) else if a=1 and b=1 and c=2 and d=2 and e=2 and f=2 then control will be (1,2)

10. else if a=2 and b=2 and c=1 and d=1 and e=2 and f=2 then control will be (1,2)
else if a=2 and b=2 and c=2 and d=2 and e=1 and f=2 then control will be (2,2) else if a=1 and b=1 and c=1 and d=1 and e=1 and f=2 then control will be (1,1)
else control will be (0,0)

11. recode any combination of a,b,c,d pair(x,y) as
if x*y=0 then output 0
else if x*y=2 then output 1
else output 2
dump out Middle Step Output as I put in the website.
for each family
"0" + line up of all parents recode_number got from step4.
"1" + line up of all children recode_number got from step4.

12. data_all.txt data_clean.txt
4. Data sets.
data_all.txt
data_clean.txt