User: naglemi

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naglemi0
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Posts by naglemi

<prev • 7 results • page 1 of 1 • next >
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
... I wish to perform resampling by bootstrapping or a similar method so that I can obtain empirical p-values for my data. The purpose of this is to correct for non-normality while avoiding overcorrection that comes with transformation of data. I'm currently using SKAT, which allows one to build null m ...
statistics gwas genesis resampling resample written 5 months ago by naglemi0
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Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
... I'm trying to figure out what the differences between AssocTestMM (in GENESIS library) and EMMAX are. I was told they are equivalent, but the results I'm getting from the two are slightly different. Should they match perfectly? What is the cause of the differences? Thank you. ...
gwas genesis assoctestmm written 7 months ago by naglemi0 • updated 7 months ago by mconomos30
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Comment: C: GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for thi
... Thank you for this suggestion. I've gotten it to work with a modification of the approach you suggested, and am now trying to figure out how to avoid this roundabout method. When I create a column for sex and set them all to either M or F, I get the following: > assoc <- assocTestMM(genoData ...
written 9 months ago by naglemi0
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Unable to build GDS with more than 255 scaffolds?
... I'm preparing to run assocTestMM (GENESIS) but first need to have a GDS file prepared by snpgdsBED2GDS. I'm working with a nonmodel organism that has 19 autosomes and over 1000 scaffolds which are not assigned to any autosome. Interestingly, my GDS files seem to be capped at 255 scaffolds and everyt ...
gwas gds genesis written 9 months ago by naglemi0 • updated 9 months ago by zhengx30
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GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
... I'm working with a species that does not have sex chromosomes. The only part of the workflow in which I see I can note this is while building the GRM – by setting the option autosome.only to TRUE. I've looked through R documentation for assoctestMM and don't see a way to specify that there are no se ...
gwas genesis assoctestmm written 11 months ago by naglemi0 • updated 11 months ago by mconomos30
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Comment: C: Why is assocTestMM running with only a fraction of SNPs in genotype data?
... Thanks for the quick response! I misunderstood that option and thought it asked for the number of chromosomes. After removing the option chr, I'm able to run the whole SNP set.  ...
written 11 months ago by naglemi0
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Why is assocTestMM running with only a fraction of SNPs in genotype data?
... I'm trying to run assocTestMM (GENESIS) with 4.4M SNPs. However, it runs with only a small fraction of SNPs. I've read the R documentation for assocTestMM and don't see any type of filter settings. I checked my genotype data prior to running assocTestMM and made sure the correct number of SNPs are i ...
gwas genesis lmm assoctestmm written 11 months ago by naglemi0 • updated 11 months ago by mconomos30

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