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weizhouUMICH / SAIGE

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correlation between step 1 and step2 in SAIGE-GENE #135

Closed wym0072003 closed 4 years ago

wym0072003 commented 4 years ago

Hi Wei,

I am applying SAIGE-GENE on my data recently. I have a simple question on the correlation between step 1 and step2. From my understanding, some output files result from step1 should be the input files in step2. However, I can't figure out which output files in step1 are the inputs for step2. Can you please specify those files, thus we can easily check if we have already get outputs and inputs successfully in managing the process. Thanks very much!

Best,

Yiming

weizhouUMICH commented 4 years ago

Hi Yiming, Sorry for my late reply. Through this link, you may find the list of input files for step 2 for SAIGE-GENE: https://github.com/weizhouUMICH/SAIGE/wiki/Genetic-association-tests-using-SAIGE#input-files-3

3, 4, and 6 are files from step 1 which are model file (.rda), the variance ratio file (.varianceRatio.txt), and the sparse Sigma file (.sparseSigma.mtx)

Thanks! Wei

wym0072003 commented 4 years ago

Thanks very much Wei! I have got the final results from SAIGE-GENE. Not sure why only output a subset of genes in the group file (not all genes). I gusse using default setting for MAF filters will force saige to consider all input variants? --minMAC=0.5 means variants with allele count >=1 will be used in the test, that's right?

Best regards

Yiming

weizhouUMICH commented 4 years ago

Hi Yiming,

Yes, --minMAC=0.5 is to exclude monomorphic variants. minMAC and minMAF (whichever is higher ) are used to specify the minimum frequency for markers, maxMAFforGroupTest is for maximum MAF. minInfo is used for minimum imputation info if the markers are imputed.

Thanks, Wei

On Thu, Feb 27, 2020 at 10:19 PM wym0072003 notifications@github.com wrote:

Thanks very much Wei! I have got the final results from SAIGE-GENE. Not sure why only output a subset of genes in the group file (not all genes). I gusse using default setting for MAF filters will force saige to consider all input variants? --minMAC=0.5 means variants with allele count >=1 will be used in the test, that's right?

Best regards

Yiming

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wym0072003 commented 4 years ago

Thanks very much Wei! Hope you are safe and well.

Best regards

Yiming