custom annotations with annotatr
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luca.s ▴ 50
@lucas-24386
Last seen 7 months ago
Italy

Hi, I am trying to use annotatr with custom annotations from a bed file to annotate differentially methylated regions. the bed has the following columns: chr, start, end, name (enst), score, strand, enst, entrez_ID, gene_name. I have tried a couple of options but did not manage to have the enst, entrez_ID, gene_name in the annotations. Below are my attempts and corresponding errors. Any advise on how to solve this? Thanks

#When I try this code:
extraColsAn = c(tx_id='character', gene_id='numeric', symbol='character')
read_annotations(con = ".annotations/TSS1500.bed", genome = 'hg38', extraCols = "extraColsAn", name = 'TSS1500', format = 'bed')
#it gives me this error:
#Error in .local(con, format, text, ...) : 
# 'extraCols' must have valid names

#when I omit extraCols
read_annotations(con = ".annotations/TSS1500.bed", genome = 'hg38',
                 #extraCols = "extraColsAn",
                 name = 'TSS1500', format = 'bed')
#the error is:
#Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
# scan() expected 'an integer', got 'ENST00000456328.2'

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
annotatr • 510 views
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Entering edit mode

solved, just overlooked.... ``

extraColsAn = c(tx_id='character', gene_id='character', symbol='character')
read_annotations(con = ".annotations/TSS1500.bed", genome = 'hg38', extraCols = "extraColsAn", name = 'TSS1500', format = 'bed')
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