Get Germline variants from Biomart

Question

[Sharon]

Hi Everyone

I am trying to get all genes that has gremlin variant from biomart using code:

SNPs <- getBM(attributes=c('ensembl_gene_id'), filters = 'germ_line_variation_source',values='with_validated_snp', mart = mygenome)

SNPs <- getBM(attributes=c('ensembl_gene_id'), filters = 'germ_line_variation_source',values=’SGRP’, mart = mygenome)

SNPs <- getBM(attributes=c('ensembl_gene_id'), filters = 'germ_line_variation_source',values=TRUE, mart = mygenome)

all the above fails. Although, something similar works with me for GO:

GO <- getBM(attributes=c('ensembl_gene_id'), filters = 'go', values ="GO:0006119", mart = mygenome)

Any hint how to use the snps filter?

Thanks

Answer 1

[Sharon]

Hi everyone

In case anyone else stuck at this like me, this works:

SNPs <- getBM(attributes=c('ensembl_gene_id', 'germ_line_variation_source'),filters = 'germ_line_variation_source',values='SGRP', mart = mygenome)

Thanks

[Ram]

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[Sharon]

Thanks RamRS, done :)

[Ram]

Your query #2 in the question should work as well. I have a feeling the quotes interfere with the query. If you're copy-pasting from Microsoft products (or other word processors), ensure all quotes are simple single or double quotes (' and ") and not stylized quotes ( ’ ).

See the difference here:

## first line is your query, second line is mine
SNPs <- getBM(attributes=c('ensembl_gene_id'), filters = 'germ_line_variation_source',values=’SGRP’, mart = mygenome)
SNPs <- getBM(attributes=c('ensembl_gene_id'), filters = 'germ_line_variation_source',values='SGRP', mart = mygenome)

[GenoMax]

ensure all quotes are simple single or double quotes (' and ") and not stylized quotes ( ’ ).

Second that. Turn off "smart quotes and dashes" in Apple --> System Preferences --> Keyboard --> text, if you are using macOS.

[Sharon]

I am using linux, and vim. :) Thanks genomax