Sentence examples for using the ld command from inspiring English sources

Pairwise linkage disequilibrium (LD) between rs2075650 and the APOEε2/ε3/ε4 polymorphism determining SNPs rs7412 and rs429358 was calculated in 8946 individuals using the –ld command in PLINK (http://pngu.mgh.harvard.edu/purcell/plink, (Purcell et al., 2007)).

We generated a smaller set of 41 692 autosomal SNPs (successfully genotyped in >95% of individuals, with a Hardy Weinberg equilibrium test P-value >10−8, with minor allele frequencies >0.4 and pruned to show low levels of LD using the PLINK command '–indep 50 5 2') that were used to check relationships/sample duplications and ethnicities.

To adjust for population stratification, we first performed principal component analysis (PCA) using the smartpca routine of the EIGENSOFT package [Price et al., 2006] on 139,445 autosomal SNPs (pruned to be in low levels of LD with one another using the PLINK command "–indep 50 502").

The analysis was performed using the MCM command UAMCM.

We analysed the imputed data using the micombine command [ 29].

The time measurement was obtained using the Unix command 'time'time

Weighting was applied using the 'ccode' command in TNT.

Normality was visually inspected using the "normplot" command in Matlab.

These estimates were obtained from PLINK, using the "–het" command.

Mean values were extracted using the " fslmeants" command.

This was done using the CERR command downSampleScan.