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Now, using the residualized phenotypes in a .ped file please specify the --makeResiduals and --inverseNormalize options. These will correct for the intercept and then inverse-normalize the phenotype prior to conducting association tests.
Now, using the residualized phenotypes in a .ped file please specify the --makeResiduals and --inverseNormalize options. These will correct for the intercept and then inverse-normalize the phenotype prior to conducting association tests.
'''Marker Grid for Fast-LMM Empirical Kinship: '''
'''Marker Grid for Fast-LMM Empirical Kinship'''
If you plan to use the Fast-LMM mixed model capability in Rare-Metal-Worker, it is likely preferable that you construct your kinship matrix either 1) with genome-wide markers from a GWAS panel (or 2nd generation exome chip) or 2) a subset of selected markers from the exome chip array. A list of markers can be obtained from Scott. There are many common markers on the first version of the exome chip, and many were selected for fine mapping (of MHC) or because of prior GWAS signals. These markers would ideally be excluded from the set of markers used to construct the empirical kinship matrix.
If you plan to use the Fast-LMM mixed model capability in Rare-Metal-Worker, it is likely preferable that you construct your kinship matrix either 1) with genome-wide markers from a GWAS panel (or 2nd generation exome chip) or 2) a subset of selected markers from the exome chip array. A list of markers can be obtained from Scott. There are many common markers on the first version of the exome chip, and many were selected for fine mapping (of MHC) or because of prior GWAS signals. These markers would ideally be excluded from the set of markers used to construct the empirical kinship matrix.
'''Running Times: '''
'''Running Times'''
In samples of a few thousand rare-metal-worker should take less than 20 minutes to complete. In larger samples (~10,000 or more with phenotype data) it can take several days to complete an exome-chip-wide scan.
In samples of a few thousand rare-metal-worker should take less than 20 minutes to complete. In larger samples (~10,000 or more with phenotype data) it can take several days to complete an exome-chip-wide scan.
'''Submitting Results for Meta-Analysis: '''
'''Submitting Results for Meta-Analysis'''
All output files from Rare-Metal-Worker can then be uploaded to an sftp server at the University of Michigan for central analysis -- please email [mailto:svrieze@umich.edu Scott Vrieze] for the hostname, username, and password.
All output files from Rare-Metal-Worker can then be uploaded to an sftp server at the University of Michigan for central analysis -- please email [mailto:svrieze@umich.edu Scott Vrieze] for the hostname, username, and password.
