r2 calculation

[nakanoma...@gmail.com]

Hello, everyone.

I tired to calculate r2 value following the command.

/plink-1.07-mac-intel/plink --file test --nonfounders --r2

But I got following the log and plink.ld file.

Are there any problems in ped and map files, or command.

Need help! Thank you very much!

Writing this text to log file [ plink.log ]

Analysis started: Tue Sep 13 10:04:59 2016

Options in effect:

--file test

--nonfounders

--r2

5 (of 5) markers to be included from [ test.map ]

5 individuals read from [ test.ped ] 

5 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

3 cases, 2 controls and 0 missing

5 males, 0 females, and 0 of unspecified sex

Before frequency and genotyping pruning, there are 5 SNPs

0 founders and 5 non-founders found

Total genotyping rate in remaining individuals is 1

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 5 SNPs

After filtering, 3 cases, 2 controls and 0 missing

After filtering, 5 males, 0 females, and 0 of unspecified sex

Writing LD statistics to [ plink.ld ] 

plink.ld

 CHR_A         BP_A     SNP_A  CHR_B         BP_B     SNP_B           R2 

test.map

1 snp0001 0 166056

1 snp0002 0 166527

1 snp0003 0 167151

1 snp0004 0 1037271

1 snp0005 0 5335002

test.ped

FAM001 1 1 2 1 1 A A A A A A A A A A

FAM001 2 1 2 1 1 A A A A A A T T G G

FAM002 3 1 2 1 2 G G G G G G T T A A

FAM002 4 1 2 1 2 G G G G G G T T A A

FAM002 5 1 2 1 2 A A A A A A A A A A

[Josef Frank]

PLINK only uses founders for LD calculations. Since in your file set there are no founders (denoted by "0" in the 3rd and 4th columns) LD calculation gets skipped. Newer builds provide a warning here: "Warning: Skipping --r2 since there are less than two founders."

Best wishes
Josef

BTW: Your pedigree structure shows severe issues: In your example file Person "FAM001 2" should have female sex, and also all members of "FAM001" seem to be their own parents. Likewise in "FAM002" there are parents referenced that are not present in the data set

P.S.: maybe a plink subroutine for checking/fixing pedigree structure would come handy here