User: johnS

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johnS0
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Posts by johnS

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Understanding sickle cell trait
... I am new to genomic world, so my questions might be bit silly. I been reading about it a lot recently and still I get confused with few things. And I feel if I am able to find answer for this, then I will be able to relate things. The sickle cell anemia is what I took as an example Here is my und ...
genome gene alleles rna-seq snp written 10 days ago by johnS0
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How plink calculates meta-analysis
... I am trying to find the logic/calculation what is used in plink to calculate the meta analysis when run the following command plink --meta-analysis study1.assoc study2.assoc study3.assoc I checked the plink website but dint find details http://zzz.bwh.harvard.edu/plink/metaanal.shtml . Could someo ...
gwama metal meta-analysis plink written 3 months ago by johnS0 • updated 12 weeks ago by Biostar ♦♦ 20
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Comment: C: How to retrieve Gene name from SNP ID using biomaRt
... @kevin Blighe Thank you :-) May I know why ENSG00000143921 got ABCG8 and ABCG5,ABCG8 ? In gsnpense its only ABCG8 ...
written 5 months ago by johnS0
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Comment: C: How to retrieve Gene name from SNP ID using biomaRt
... @kevin Blighe Thank you. I tried it for this for snp rs6544713 getBM(attributes=c( "ensembl_gene_stable_id"), filters="snp_filter", values="rs6544713", mart=ensembl, uniqueRows=TRUE) But this is giving me only the Ensembl gene ID-s, If I lookup for the same SNP in https://biit.cs.ut.ee/gsnpe ...
written 5 months ago by johnS0
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How to retrieve Gene name from SNP ID using biomaRt
... I am trying to get gene name from the SNP ID, I came across some posts and came up with this, but I am getting an error Here is my code library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") getBM(attributes = c("external_gene_name"), filters = "snp_fil ...
gene R biomart rsid snp written 5 months ago by johnS0 • updated 5 months ago by Kevin Blighe37k

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