Since it does not need to keep the entire x correlation matrix in memory, it is usually capable of handling 6-digit window sizes well outside -indep's reach.įinally, -indep-pairphase is just like -indep-pairwise, except that its r 2 values are based on maximum likelihood phasing (like "-r2 dprime" below). Its third parameter is a pairwise r 2 threshold: at each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain. indep-pairwise takes the same first two parameters as -indep. The top panels show the longest span scores at CI-E the. In a backward digit span task, the procedure is largely the same, except that subjects being tested are asked to recall the digits in backward order ( e. The ordinate shows the frequency (number of children) while the abscissa shows the longest digit span length correctly recalled. Additionally, based on a bifactor model of the W AIS-IV, Gignac (2014) reported a. See the PLINK 1.07 documentation for some discussion of parameter choices. Frequency distributions for the WISC III longest digit span forward and digit span backward scores at CI-E (age 8 0 to 9 11) and CI-HS (age 15 0 to 18 6). suggested that the correlation between Digit Span Backward and fluid intelligence was. At each step, all variants in the current window with VIF exceeding the threshold are removed. This study examined performance in the forward and backward digit span task of the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) in a large group of children with specific learning disorder (SLD) as compared with a group of typically developing children matched for age and sex. It assesses childrens ability to hold information in short-term memory and. indep requires three parameters: a window size in variant count or kilobase (if the ' kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. The Digit Span Task (Backwards-Only Child Version) measures working memory. (Results may be slightly different from PLINK 1.07, due to a minor bugfix in the r 2 computation when missing data is present, and more systematic handling of multicollinearity.) Output files are valid input for -extract/-exclude in a future PLINK run. They are currently based on correlations between genotype allele counts phase is not considered. prune.in (and the IDs of all excluded variants to plink. These commands produce a pruned subset of markers that are in approximate linkage equilibrium with each other, writing the IDs to plink. To maximize backward compatibility, we have replicated this quirk. If your dataset has a shortage of them, -make-founders may come in handy. Note that Haploview/PLINK 1.07 has a minor quirk in its handling of the low CI bound: a potential haploblock's outermost variant pair is considered to be in 'strong LD' even if the bottom of its D-prime confidence interval is exactly equal to the -blocks-strong-lowci value. PLINK 1.9 includes much faster implementations of PLINK 1.07's LD-based variant pruner and haplotype block estimator, and commands to explicitly report LD statistics.Īll of the following calculations only consider founders.
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