User: GENOMIC_region

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Posts by GENOMIC_region

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Sporadic missingness with admixmmap
... I'm running into an issue with sporadic missingness when using admixmmap function from Genesis. Column `rsids` joining factor and character vector, coercing into character vector Reading in Phenotype and Covariate Data... Fitting Model with 7485 Samples Computing Variance Component ...
genesis admixmap written 4 weeks ago by GENOMIC_region0 • updated 4 weeks ago by Stephanie M. Gogarten710
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Comment: C: BioMart : Error in getBM, the BioMart webservice returned an invalid result
... Received same error couple hours back today. ...
written 4 months ago by GENOMIC_region0
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Comment: C: Genesis: doubts with admixMAPMM
... Thank you. That helps. Is `Stat joint` Joint.beta? (hopefully this is last question. :) ) ...
written 5 months ago by GENOMIC_region0
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Comment: C: Genesis: doubts with admixMAPMM
... Thank you very much for helping me with these doubts. :) Is it possible to have beta in this analysis? If so, then It would be great to see it in future releases. ...
written 5 months ago by GENOMIC_region0
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Comment: C: Genesis: doubts with admixMAPMM
... Hi, Thank you for clarifying. :) Sorry, for not being clearer regarding my doubt in data structure. `gds.afr` has certain attributes such as snp.id, position and position also, **genotype**. ``` gds.afr <- GdsGenotypeReader(gds, genotypeVar="dosage_afr") gds.afr File: /tmp/Rtmpt27CXN/file7 ...
written 5 months ago by GENOMIC_region0
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Comment: C: Genesis: doubts with admixMAPMM
... Hi, Thank you for clarifying. :) Sorry, for not being clearer regarding my doubt in data structure. `gds.afr` has certain attributes such as snp.id, position and position also, **genotype**. ``` gds.afr <- GdsGenotypeReader(gds, genotypeVar="dosage_afr") gds.afr File: /tmp/Rtmpt27CXN/file7 ...
written 5 months ago by GENOMIC_region0
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Comment: C: Genesis: doubts with admixMAPMM
... It's true that K-1 ancestries must be used in analysis, otherwise the matrix generated would be non-invertible. Example in manual (Page 5) uses three ancestries, that's why I used three in my data due to three-way admixture present in individuals. dosage_eur <- sample(0:2, nsnp*nsamp, repla ...
written 5 months ago by GENOMIC_region0
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Comment: C: Genesis: doubts with admixMAPMM
... Dear Stephanie, Thank you very much for your prompt and detailed reply. Can you please help with genotype variable in gds data structure (Question 2.a 2.b and 2.c)? Or, as stated: > The admixMapMM and admixMap functions will only use data from the > nodes you specify with the genotypeVar ...
written 5 months ago by GENOMIC_region0
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Genesis: doubts with admixMAPMM
... Hello devels/users, I'm interested in using GENESIS package for admixMapMM function to perform local ancestry association on data on a three-way admixed population. I've inferred local ancestry using RfmixV1. I know location of each SNP, name and per ancestry dosage (0,1,2) information per perso ...
genesis admixmap written 5 months ago by GENOMIC_region0 • updated 5 months ago by Stephanie M. Gogarten710
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Comment: C: HOW TO USE LIMMA PACKAGE
... Do you've case control study design? ...
written 6 months ago by GENOMIC_region0

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Popular Question 9 months ago, created a question with more than 1,000 views. For status was 'Couldn't connect to server': bioClite
Voter 11 months ago, voted more than 100 times.
Supporter 16 months ago, voted at least 25 times.

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