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ShihChingYu / TransAT

TransAT is a package within the R programming language for converting RefSeq ID to Ensembl transcripts and mapping the genomic position, followed by providing variant allele frequencies and gene annotations.
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Error in `$<-.data.frame`(`*tmp*`, "CDS_start_loc", value = c(6705L, 293L, : replacement has 14783 rows, data has 14152 #1

Open njtourtillott opened 2 years ago

njtourtillott commented 2 years ago

Hi,

I tried using your package to map Refseq ID's to genomic position, however when running convert_transcriptID(dat, db, dat_filter = "refseq_mrna") on my data I got this error: Error in $<-.data.frame(*tmp*, "CDS_start_loc", value = c(6705L, 293L, : replacement has 14783 rows, data has 14152 -- indicating that the function was trying to assign more values than my input had rows. I made sure to format my input file in the same manner described in your paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8240296/) in table 1a. Could you please take a look at this issue?

Thank you! Nick

jon4thin commented 2 years ago

I have the same issue.

Error in $<-.data.frame(*tmp*, "CDS_start_loc", value = c(992L, 981L, : replacement has 12 rows, data has 9

1 row example of my input df: refseq Nucleotide_changes NM_002137 992delG