User: landscape95

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landscape95160
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Posts by landscape95

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Estimate the genomic relationship between Discovery and Target sample in PRS
... Hi everyone, I am trying to calculate the genomic relationship between discovery and target sample but I am not sure how to make the running time affordable for large sample size (E.g 500k individuals x 1 million SNPs). Your help is really appreciated! ...
gwas prs written 7 months ago by landscape95160 • updated 7 months ago by Sam2.6k
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Comment: C: Adjusting binary phenotype (case/ctrl) for Polygenic Risk Score (PRS)
... Thank you very much, Sam! so technically when we say "adjust for phenotype" it is implicitly understand as a linear regression for the original phenotypes with all covariates, isn't it? As I have read some papers mentioned they used logistic regression for binary traits so I'm a bit confusing though ...
written 7 months ago by landscape95160
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Adjusting binary phenotype (case/ctrl) for Polygenic Risk Score (PRS)
... Hi everyone, I am a little confusing of how to adjust binary phenotype for polygenic risk score given values of covariates. For instance, in a continuous trait, we use the residual of a linear model as an adjusted phenotype. Is it ok to also use the residual of a logistic model as an adjusted phe ...
prs written 8 months ago by landscape95160 • updated 7 months ago by Sam2.6k
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Comment: C: Infer pedigree from Kinship coefficients
... This is definitely helpful. Thank you very much ...
written 9 months ago by landscape95160
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Infer pedigree from Kinship coefficients
... Hi everyone, I have a kinship file computed by KING software which contains 5 columns: ID1, ID2, HetHet, IBS0, Kinship. I also have a fam file but missing the father and mother data for each individuals. Now is there any way to recover the pedigree data from the current data I have? Your help is re ...
gwas kinship written 10 months ago by landscape95160 • updated 9 months ago by margherita.col20
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Missing lots of SNP while clumping
... Hi everyone, has anyone experienced this issue, I have around a million SNPs to do the PRS but with PRSice, after clumping, I only have around 100k SNPs remain. I wonder what situation this could be, thanks. Your help is really appreciated! Base file: plink.stat 1133273 variant(s) obser ...
prsice written 11 months ago by landscape95160
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Comment: C: Get SNP information with association test with PLINK
... Thank you so much, Chang. ...
written 12 months ago by landscape95160
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Comment: C: Get SNP information with association test with PLINK
... Thanks for your prompt reply, Here is the code and output of plink1.9: plink --bfile test --assoc --adjust --out output --allow-no-sex --threads 100 PLINK v1.90b4.1 64-bit (30 Mar 2017) Options in effect: --adjust --allow-no-sex --assoc --bfile test --out ...
written 12 months ago by landscape95160
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MTG2 error forrtl: severe (174): SIGSEGV, segmentation fault occurred
... I am calculating the mean and variance between discovery and target samples using MTG2. After I made a binary grm from plink, I used MTG2 for calculation. Has anyone experienced this problem with MTG2 before? I made sure the the id of the discovery and target samples order is the same as the grm id ...
mtg2 written 12 months ago by landscape95160 • updated 10 months ago by Biostar ♦♦ 20
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Get SNP information with association test with PLINK
... Hi everyone, Does anyone know how to get the SNP information containing CHR ID A1 REF etc with association test on quantitative trait from plink (output file: .qassoc). I done the association test and I want to obtain these information also. In --linear with plink2, I have it, but with plink1.9 ass ...
gwas plink written 12 months ago by landscape95160 • updated 12 months ago by zx87549.0k

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