User: anajacintafernandes

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CBMR, Portugal
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Posts by anajacintafernandes

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Comment: C: Get cytoband from refsnp ID using biomaRt in R
... Here's an example of a SNP that get the CHR annotation:  rs7931342 snp_locs refsnp_id chr_name chrom_start chrom_end 1 rs7931342 11 69227030 69227030 2 rs7931342 CHR_HSCHR11_1_CTG3 69230683 69230683 then, when you move to hits you get the following error: ...
written 10 weeks ago by anajacintafernandes0
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Comment: C: Get cytoband from refsnp ID using biomaRt in R
... Thanks, this is amazing! Just a few comments: 1) I needed to remove CHR annotations, otherwise I would get an error.  snp_locs <- snp_locs[grep("CHR", snp_locs$chr_name, invert = TRUE),] 2) Typo error :p ## match SNPs to cyto bands hits <- cyto[findOverlaps(query = snp_granges, ...
written 10 weeks ago by anajacintafernandes0
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Get cytoband from refsnp ID using biomaRt in R
... Hi,  Do any of you know how to get the cytoband location out of a refsnp_id through biomaRt? I'm currently using the following Marts: hsapiens <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") snpmart <- useMart("ENSEMBL_MART_SNP", dataset = "hsapiens_snp") I know that ...
biomart R written 10 weeks ago by anajacintafernandes0 • updated 10 weeks ago by Mike Smith2.1k
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Comment: C: biomaRt error when connecting to host
... Hi! Having the same problem! I guess it must be something with biomaRt and we will have to wait for them to solve it.  ...
written 7 months ago by anajacintafernandes0
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Retrieve SNP flanking sequences in biomaRt
... Hi,  I can't retrieve the flanking regions of my snps. I used: snpmart<- useMart("ENSEMBL_MART_SNP",dataset = "hsapiens_snp") TEST<- getBM(attributes = c("refsnp_id","upstream_flank","downstream_flank"), filters = c("snp_filter","upstream_flank","downstream_flank"), checkFilters = FALSE, v ...
snp biomart upstream_flank downstream_flank written 12 months ago by anajacintafernandes0 • updated 12 months ago by Mike Smith2.1k

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