Skip to content

Instantly share code, notes, and snippets.

@klmr

klmr/biomart.r

Last active August 29, 2015 14:10
Show Gist options
  • Save klmr/b0abf27fd33aa8c81cee to your computer and use it in GitHub Desktop.
Save klmr/b0abf27fd33aa8c81cee to your computer and use it in GitHub Desktop.
Download ZIP
BiomaRt weirdness
Raw
biomart.r
library(biomaRt)
ensembl = useMart('ensembl', dataset = 'mmusculus_gene_ensembl')
seq = getBM(c('ensembl_gene_id', 'ensembl_transcript_id', 'coding'),
filters = 'external_gene_name', values = 'HAT1', mart = ensembl)
head(seq, 1)
Raw
result
ensembl_gene_id
1 ATGGCGGCCTTGGAGAAATTTCTGGTGGAGTATAAGAGTGCCGTGGAGAAGAAACTAGCAGAGTACAAGTGTAACACCAACACAGCAATCGAGCTGAAACTAGTTCGTTTTCCTGAAGATCTTGAGAATGACATTAGAACTTTCTTTCCTGAATATACCCATCAGCTCTTTGGGGATGATGAAACTGCTTTCGGTTACAAGGGCCTGAAGATCTTGCTGTACTATATTGCTGGTAGCCTGTCAACACTGTTCCGTGTTGAATATTCATCTAAAGTTGATGAGAACTTTGATTGTGTGGAGGCAGATGATGTTGAAGGCAAAATCAGACAAATCATTCCACCTGGGTTTTGCACAAACACAAATGATTTTCTTTCCTTGCTGGAAAAGGAAACTAATTTCAAGCCTTTTGGAACCCTCCTCCATACATACACAGTTCCTAGTCAGACAGGAGGTGAAACCTTTACTTTCCAGATCCACAAGGCTGACATGACATGTAGAGGCTTTCGAGAATATCATGAAAGGCTTCAGACCTTTTTGATGTGGTTTATTGAAACTGCTAGCTTTATTGACGTGGATGATGAAAGATGGCACTACTTTCTAGTATTTGAGAAGTATAATAAGGATGGAGCTACGCTCTTTGCGACCGTAGGCTACATGACAGTCTATAATTACTATGTGTACCCAGACAAAACCCGGCCACGTGTAAGTCAGATGCTGATACTGACTCCATTTCAAGGTCAGGGCCACGGTGCTCAACTTCTTGAAACAGTTCATAGATACTACATTTCATTTCCTACAGTTCTTGATATTACAGCGGAAGATCCGTCCAG1 ATGGCGGCCTTGGAGAAATTTCTGGTGGAGTATAAGAGTGCCGTGGAGAAGAAACTAGCAGAGTACAAGTGTAACACCAACACAGCAATCGAGCTGAAACTAGTTCGTTTTCCTGAAGATCTTGAGAATGACATTAGAACTTTCTTTCCTGAATATACCCATCAGCTCTTTGGGGATGATGAAACTGCGA
ensembl_transcript_id coding
1 ENSMUSG00000027018 ENSMUST00000028408
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment