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However, only the R1 random matrices represented the same combination of nucleotide preferences, though present in distinct permutations as compared to the original matrices.
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The three LD-based methods using Haploview are the least conservative, with significance thresholds between 2.72 × 10-7 and 3.71 × 10-7, corresponding to α levels between 0.15 and 0.20 as compared to permutation testing using PRESTO (see Table 1).
Using Poisson-binomial statistics (Wang, 1993), PART can be used for efficient and precise calculation of small P-values, as compared with the permutation approach.
Although sample sizes will affect runtime of deGPS, it is worth noting that as compared with other methods, permutation-based DE detection implemented in deGPS is robust against different sample sizes.
Only those TFBSs are extracted that occur less frequently in 95% of permutation tests than in the original distribution (corresponding to a p-value < 0.05 to observe the original distribution by chance) and that corresponds to at least a twofold increase in their density in the original distribution as compared with an average pair density in permutation tests.
As seen from the data, the strong interdependencies between copy loss and copy gain clearly justifies our joint modeling as compared to simple marginal approach with or without permutation procedures.
The set of rich club regions exhibited significantly higher levels of the GI as compared to the set of non-rich club regions (P = 0.007; 10 000 permutations; Fig. 2).
It then uses standard hypothesis testing to determine which model profiles have significantly more genes assigned as compared to the average number of genes assigned to the model profile in the permutation runs.
as compared with control fish.
Kibbeh is a dish found throughout the Middle East and regional permutations, as well as numerous transliterations – kibbeh, kubba, kubi – abound.
To explore how circular permutations perform compared with random permutations, alternative permutation strategies were applied to the distance 0 dataset.
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