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, 13:53, 1 April 2014
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| where <math>l</math> is the count of variants, <math>G_i</math> and <math>f_i</math> are the genotype vector and estimated allele frequency for the <math>i^{th}</math> variant, respectively. Each element in <math>G_i</math> encodes the minor allele count for one individual. Model parameters <math>\hat{\boldsymbol{\beta}}</math>, <math>\hat{\sigma_g^2}</math> and <math>\hat{\sigma_e^2}</math>, are estimated using maximum likelihood and the efficient algorithm described in [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1681.html Lippert et. al]. For convenience, let the estimated covariance matrix of <math>\mathbf{y}</math> be <math>\hat{\boldsymbol{\Omega}}=\hat{\sigma_g^2}\mathbf{K}+\hat{\sigma_e^2}\mathbf{I}</math>. | | where <math>l</math> is the count of variants, <math>G_i</math> and <math>f_i</math> are the genotype vector and estimated allele frequency for the <math>i^{th}</math> variant, respectively. Each element in <math>G_i</math> encodes the minor allele count for one individual. Model parameters <math>\hat{\boldsymbol{\beta}}</math>, <math>\hat{\sigma_g^2}</math> and <math>\hat{\sigma_e^2}</math>, are estimated using maximum likelihood and the efficient algorithm described in [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1681.html Lippert et. al]. For convenience, let the estimated covariance matrix of <math>\mathbf{y}</math> be <math>\hat{\boldsymbol{\Omega}}=\hat{\sigma_g^2}\mathbf{K}+\hat{\sigma_e^2}\mathbf{I}</math>. |
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− | ==Chromosome X== | + | ==ANALYZING MARKERS ON CHROMOSOME X== |
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| To analyze markers on chromosome X, we fit an extra variance components <math> {{\sigma_g}_X}^2 </math>, to model the variance explained by chromosome X. A kinship for chromosome X, <math> \boldsymbol{K_X} </math>, can be estimated either from a pedigree, or from genotypes of marker from chromosome X. Then the estimated covariance matrix can be written as <math>\hat{\boldsymbol{\Omega}}=\hat{\sigma_g^2}\mathbf{K}+\hat{{\sigma_g}_X^2}\mathbf{K_X}+\hat{\sigma_e^2}\mathbf{I}</math>. | | To analyze markers on chromosome X, we fit an extra variance components <math> {{\sigma_g}_X}^2 </math>, to model the variance explained by chromosome X. A kinship for chromosome X, <math> \boldsymbol{K_X} </math>, can be estimated either from a pedigree, or from genotypes of marker from chromosome X. Then the estimated covariance matrix can be written as <math>\hat{\boldsymbol{\Omega}}=\hat{\sigma_g^2}\mathbf{K}+\hat{{\sigma_g}_X^2}\mathbf{K_X}+\hat{\sigma_e^2}\mathbf{I}</math>. |