CODEWITHSUNDEEP
rbioinformaticsdna-sequencegenome
Carla Flores
Carla Flores

Reputation: 33

How to solve these errors: slot of x need be populated with unique names, or subscript contains out-of-bounds indices, using predORF?

I am having some problems with this function predORF

  sqa <- c("CAGGGCACCTGGCCTTGGGATGCGCCTCCTGCCCGCTGAGCCCAGGGGCCGCTATGGCCCTTCTGGCCATGCTGGCGCTGCAGACAGCTCTCTACCTAGTAGGCTTCTTCTACCCGCCGGGAGGCATATGGCGCTGGATCACCCGGGAC") 
  print(sqa)

First, I transformed the sequence into the input formats

  dnastring = DNAString(sqa) 
  print(dnastring)

  dna <- DNAStringSet(sqa) 
  print(dna)

When I use DNAstrings format:

    predORF(dnabase, n = 1, type = "grl", 
    mode = "orf", strand = "sense", 
    longest_disjoint=FALSE, 
    startcodon = c("ATG"), 
    stopcodon = c("TAA"))

I got this error

  Error in predORF(dnastring, n = 1, type = "grl", mode = "orf", strand = "sense",  : 
  Sequence name slot of x need be populated with unique names.

When I define its length, i got this:

    predORF(dna[:149], n = 1, type = "grl", 
    mode = "orf", strand = "sense", 
    longest_disjoint=FALSE, 
    startcodon = c("ATG"), 
    stopcodon = c("TAA"))

  Error in predORF(dnastring[1:149], n = 1, type = "grl", mode = "orf",  : 
  Sequence name slot of x need be populated with unique names.

When I use DNAStringSet format:

    predORF(dna, n = 1, type = "grl", 
    mode = "orf", strand = "sense", 
    longest_disjoint=FALSE, 
    startcodon = c("ATG"), 
    stopcodon = c("TAA"))

I got this error

  Error in predORF(dna n = 1, type = "grl", mode = "orf", strand = "sense",  : 
  Sequence name slot of x need be populated with unique names.

When I define its length, i got this:

    predORF(dna[:149], n = 1, type = "grl", 
    mode = "orf", strand = "sense", 
    longest_disjoint=FALSE, 
    startcodon = c("ATG"), 
    stopcodon = c("TAA"))

  Error: subscript contains out-of-bounds indices

How can I solve this issue?

Thanks in advance!

Upvotes: 1

Views: 72

Answers (1)

Ventrilocus
Ventrilocus

Reputation: 1488

the problem is that predORF needs named sequences as input. See below:

library(Biostrings)
library(systemPipeR)

sqa <- c("ATGTAA")
sqb <- c("ATGGCCTAA")
dna <- DNAStringSet(c(seq_a = sqa, seq_b = sqb), use.names = T) 
predORF(dna, n = 1, type = "grl", 
        mode = "orf", strand = "sense", 
        longest_disjoint=FALSE, 
        startcodon = c("ATG"), 
        stopcodon = c("TAA"))

Upvotes: 2

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