Question

Cannot return precursor info in package miRBaseConverter

0

Entering edit mode

gzbyzyx2011 • 0

@gzbyzyx2011-23847

Last seen 23 months ago

United States

Hi,

I am trying to use package miRBaseConverter to do some analysis for my project. When I input my code as followed

library(miRBaseConverter)
hsa_precursor <- getAllMiRNAs(version="v22", type="precursor", species="hsa")

I get no results back.

hsa_precursor [1] Accession Name Sequence <0 rows> (or 0-length row.names)

But if I use replace "precursor" with "mature", I got the info back successfully.

head(getAllMiRNAs(version="v22", type="mature", species="hsa"))

Accession            Name               Sequence
  
1 MIMAT0010195 hsa-let-7a-2-3p CUGUACAGCCUCCUAGCUUUCC 2 MIMAT0004481 hsa-let-7a-3p CUAUACAAUCUACUGUCUUUC 3 MIMAT0000062 hsa-let-7a-5p UGAGGUAGUAGGUUGUAUAGUU 4 MIMAT0004482 hsa-let-7b-3p CUAUACAACCUACUGCCUUCCC 5 MIMAT0000063 hsa-let-7b-5p UGAGGUAGUAGGUUGUGUGGUU 6 MIMAT0026472 hsa-let-7c-3p CUGUACAACCUUCUAGCUUUCC

Any ideas or suggestions?

Thanks, Yixin

miRBaseConverter precursor getAllMiRNAs • 759 views

ADD COMMENT • link 4.4 years ago gzbyzyx2011 • 0

1

Entering edit mode

There's a bug in getAllMiRNAs

debug: ind <- which(apply(MiRNAs, 1, function(x) allis.na(x))))
Browse[2]> MiRNAs[1:3,]
   Accession  Name Sequence
58        60 43728     1153
59        61 43729     1154
60        62 43732     1155
Browse[2]> 
debug: MiRNAs = MiRNAs[-ind, ]
Browse[2]> length(ind)
[1] 0
Browse[2]> 
debug: MiRNAs = unique(MiRNAs)
Browse[2]> dim(MiRNAs)
[1] 0 3

Please notify the author. If you use 'all' and 'mature' and take the difference you may get what you want

> dim(hsa_mat)
[1] 2656    3
> dim(hsa_all)
[1] 4573    3
> 4573-2656
[1] 1917

ADD REPLY • link 4.4 years ago Vincent J. Carey, Jr. 6.7k