samreenzafer

Is this overfitting? PRScise-2

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   [DILIN.Sakaue2021.GCST90018798.noMHC.log](https://github.com/choishingwan/PRSice/files/8547491/DILIN.Sakaue2021.GCST90018798.noMHC.log) Hi I'm using PRSice-2 to run 100s & 1000s of traits from various studies from GWAS Catalog...

Hi I have run rvtest several times for single variant and grouped tests, and am now trying to use the --meta score,cov for 3 populations of my cohort separately (Afr,...

When both these options are used in the rvtest command --peopleExcludeID and --freqUpper , Does rvtest first exclude the samples listed, and then calculate the new allele frequency at sites,...

I'm analyzing the rare variants in msigdb pathways using set based input. Example of the `setFile` ` GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS 1:10399063-10399125,1:10399063-10399330,1:10399628-10399704,1:10400392-10400572,1:10403070-10403136,1:10404160-10404279,1:10408070-10408140,1:10411417-10411552,1:10413061-10413251,1:10416986-10417117,1:10417375-10417509,1:10418825-10418925,1:10419416-10419539,1:10419629-10420511,1:109656075-109656425,1:109656098-109656425,1:109656711-109656787,1:109657214-109657279,1:109657589-109657671,1:109657771-109657872,1:109658813-109658909,1:109658999-109659110,1:109661164-109661700,1:109661164-109661709,1:109665010-109665497,1:109668021-109668151,1:109668056-109668151,1:109668424-109668500,1:109668924-109668989,1:109669289-109669371,1:109669470-109669571,1:109671286-109671382,1:109671472-109671583,1:109674746-109675286,1:109681808-109681834,1:109683206-109683997,.....................` And for some of the pathways, as the one above, I...

Hi I just wanted to ask that if I provide overlapping regions in a set , are the variants falling in two regions considered just once (as it should be)...

Hi, We have a genotyping cohort with samples (N>5000) of multiple races, and they have been imputed using TOPMed Imputation server (https://topmedimpute.readthedocs.io/en/latest/getting-started/), because this is the largest multi-ethnic reference panel...

Hi. I would like to also get the plots for the gene centric noncoding ncRNA regions. I see that the default (NULL) would be used for `ncRNA_pos` in the `STAARpipeline-Tutorial/STAARpipelineSummary_Gene_Centric_Noncoding.r`...

Conditional analysis - Summary Gene Centric Noncoding not running to completion

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Thanks for a great easy to use tool. I've finally reached the step where I would like to do a Gene Centric Noncoding conditional analysis on some select rare variants...

inferEthnicity Not running for EPICv2.

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I'm using R/4.4.1 and sesame Version: 1.24.0 (Depends: R (>= 4.3.0) Packaged: 2024-10-30 02:54:43 UTC; biocbuild sesameData Version: 1.24.0 Depends: R (>= 4.2.0), ExperimentHub, AnnotationHub) and Packaged: 2024-10-31 17:02:50 UTC;...