A simple correction for multiple comparisons in interval mapping genome scans

By James M. Cheverud. Heredity, 2001

431 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/8327279f02a1a919b594704d5e8794734f61184e

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Citations in the corpus

A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. (2004, methodology): “…1 p 2 1 Consequently, ls for the LD correlation (D) matrix may be calculated by principal-components analysis or, more generally, by spectral decomposition (SpD), and the approach of Cheverud (2001) may be applied to obtain the effective number of independent SNPs (Meff) represented in the matrix.”
Avoiding the high Bonferroni penalty in genome-wide association studies (2009, methodology): “The M eff approach was first proposed in genetic studies by Cheverud [2001] and later refined by Nyholt [2004].”
Escaping the Bonferroni iron claw in ecological studies (2004, methodology): “This number is a reasonable approximation to the effective number of independent tests being performed (Chevereud 2001).”
Implementing false discovery rate control: increasing your power (2005, background): “The FNR can be estimated based on an estimate of the proportion of true null cases (m 0 /m in Table 1) combined with an expectation for the number of false discoveries (from an FDR controlling procedure; V/r in Table 1, Genovese and Wasserman 2002, Taylor et al. in press).”
Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix (2005, methodology): “As Cheverud (2001) explained, Equation (1) considers two extreme situations.”
Testing for an Unusual Distribution of Rare Variants (2011, background): “Many computational tools classifying coding variants regarding impact on protein function are already published In Silico Funcitonal Profiling [24] POLYPHEN [25], SIFT [26], SNPs3D [27], and Pmut [28].”
A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic (2009, background): “Note that permutation of disease status results in correct type I error even in the presence of linkage disequilibrium (LD) [29,30], although relatively low LD is expected between rare variants [26,31,32].”
Measuring Morphological Integration Using Eigenvalue Variance (2009, background): “The latter purpose was originally developed to determine the number of independent tests to calculate the significance threshold in QTL mapping based on the Bonferroni adjustment (Cheverud 2001; Nyholt 2004).”