User: Andrea_Bio

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Andrea_Bio2.3k
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Posts by Andrea_Bio

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Comment: C: Hypermetric Distribution Of Snps In Pathways
... thanks for your reply. as i suspected and you confirmed, i don't have the data for this. But i could do a distribution of the number of pfSNPs in genes or a distribution of the number of pfSNPs in pwathways. This distribution could be an indicator of places to look more closely? ...
written 5.8 years ago by Andrea_Bio2.3k
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Comment: C: Hypermetric Distribution Of Snps In Pathways
... also, I am only looking at pathways in one 'population' and not comparing a case population to a control population. In other words, I'm trying to ask, in this population which has a specific phenotype, are any of the pathways enriched for pfSNPs compared to other pathways in the same population. I' ...
written 5.8 years ago by Andrea_Bio2.3k
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Comment: C: Hypermetric Distribution Of Snps In Pathways
... I should also add in my question I was only looking at pathways in one 'population' and not comparing a case population to a control population. In other words, I'm trying to ask, in this population which have a specific phenotype, are any of the pathways enriched for pfSNPs compared to other pathwa ...
written 5.8 years ago by Andrea_Bio2.3k
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Comment: C: Hypermetric Distribution Of Snps In Pathways
... Forgot to add that, presumbably you have a '# SNPs in gene set' figure for each each individual in the case/control populations. With a pooled DNA sample I will only have one individual in the case and control populations and even that won't be truly representative of any one individual. ...
written 5.8 years ago by Andrea_Bio2.3k
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Comment: C: Hypermetric Distribution Of Snps In Pathways
... thanks for your answer. I'm not doing GWAS so I don't have any p values. In brief, is this approach suggesting that you: a) get all pathways and get all of the genes in each pathway so that each pathway is a gene set; b) find the number of SNPs in each gene set; c) use a test to see which gene sets ...
written 5.8 years ago by Andrea_Bio2.3k
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Comment: C: Hypermetric Distribution Of Snps In Pathways
... Thanks for your answer. I am not doing GWAS studies so I don't have any P values or a problem of assigning a SNP to a gene (the SNP is either in it or very close to be in the gene). Is the GSEA enrichment technique still relevant as it doesn't take into account the fact that a gene with multiple SNP ...
written 5.8 years ago by Andrea_Bio2.3k
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Hypermetric Distribution Of Snps In Pathways
... Hello I'm really embarassed asking this question since I haven't done statistics since I was at school (and I'm a female so I'm not saying how long ago that was). I have SNPs for 2 species of cow which have a different phenotype. The SNPs were obtained from a pooled data set of 10 individuals from ...
pathway snp statistics written 5.8 years ago by Andrea_Bio2.3k • updated 3.6 years ago by Biostar ♦♦ 10
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Comment: C: Dbsnp In Vcf Format
... genotypes would be good but not essential ...
written 5.8 years ago by Andrea_Bio2.3k
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Comment: C: Dbsnp In Vcf Format
... i need genotypes too ...
written 5.8 years ago by Andrea_Bio2.3k
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Dbsnp In Vcf Format
... Hello I have seen that dbSNP makes human SNP data available in VCF 4.0 format but not for other organisms. I would like to have bovine SNP data in VCF format for use with VCFTools. Does anyone have any experience of converting dbSNP XML or ASN1 into VCF? Is there a resource available to do this? O ...
vcf format dbsnp written 5.8 years ago by Andrea_Bio2.3k • updated 5.7 years ago by Rituriya0

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