Re: [R] Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer'
Sorry - I figured that this to be a more common defined error than anything
specific to the data/function... Thanks for looking at this.
The data and function are below. Creating a single line of the data.frame at
a time will work (i.e. fold(s))
For multiple line data.frames, an error is generated. Ideally I would like
to record the output from fold(sq) in a two column data.frame, whether it
requires reading in the data to fold one line at a time or in bulk.
library(GeneRfold)
s- ATTATGCATCGACTAGCATCACTAG
fold(s)
[[1]]
[1] .....
[[2]]
[1] -2.3
sq - data.frame(c(ATGTGTGATATGCATGTACAGCATCGAC,
+ ACTAGCACTAGCATCAGCTGTAGATAGA,
+ ACTAGCATCGACATCATCGACATGATAG,
+ CATCGACTACGACTACGTAGATAGATAG,
+ ATCAGCACTACGACACATAGATAGAATA))
fold(sq)
Error in fold(sq) :
STRING_ELT() can only be applied to a 'character vector', not a 'list'
struct - t(as.data.frame(sapply(sq[,1], fold, t=37)))
Error in FUN(X[[1L]], ...) :
STRING_ELT() can only be applied to a 'character vector', not a 'integer'
dput(fold,file=fred123)
function (s, t = 37)
{
.Call(foldR, s, t, PACKAGE = GeneRfold)
}
dput(sq)
structure(list(c..ATGTGTGATATGCATGTACAGCATCGACACTAGCACTAGCATCAGCTGTAGATAGA...
= structure(c(4L,
1L, 2L, 5L, 3L), .Label = c(ACTAGCACTAGCATCAGCTGTAGATAGA,
ACTAGCATCGACATCATCGACATGATAG,
ATCAGCACTACGACACATAGATAGAATA, ATGTGTGATATGCATGTACAGCATCGAC,
CATCGACTACGACTACGTAGATAGATAG), class = factor)), .Names =
c..ATGTGTGATATGCATGTACAGCATCGACACTAGCACTAGCATCAGCTGTAGATAGA...,
row.names = c(NA,
-5L), class = data.frame)
dput(s)
ATTATGCATCGACTAGCATCACTAG
sessionInfo()
R version 2.11.0 (2010-04-22)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GeneRfold_1.6.0 GeneR_2.18.0
loaded via a namespace (and not attached):
[1] tools_2.11.0
--
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Re: [R] Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer'
Hello, sedm1000 wrote: Sorry - I figured that this to be a more common defined error than anything specific to the data/function... Thanks for looking at this. The data and function are below. Creating a single line of the data.frame at a time will work (i.e. fold(s)) For multiple line data.frames, an error is generated. Ideally I would like to record the output from fold(sq) in a two column data.frame, whether it requires reading in the data to fold one line at a time or in bulk. library(GeneRfold) s- ATTATGCATCGACTAGCATCACTAG fold(s) [[1]] [1] ..... [[2]] [1] -2.3 sq - data.frame(c(ATGTGTGATATGCATGTACAGCATCGAC, + ACTAGCACTAGCATCAGCTGTAGATAGA, + ACTAGCATCGACATCATCGACATGATAG, + CATCGACTACGACTACGTAGATAGATAG, + ATCAGCACTACGACACATAGATAGAATA)) fold(sq) Error in fold(sq) : STRING_ELT() can only be applied to a 'character vector', not a 'list' struct - t(as.data.frame(sapply(sq[,1], fold, t=37))) Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer' This appears to be a Bioconductor package, so if this doesn't help, I'd ask on the specific bioconductor mailing list. I don't have the package installed, so take the following advice with that in mind. Did you look at the str(sq) ? It is not a character vector, it is a factor, so you might need to convert or see stringsAsFactors in ?options. Try lapply(sq[, 1], function(x) fold(as.character(x))) If that doesn't work, try the other list. Good luck, Erik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer'
On May 23, 2010, at 3:27 AM, Erik Iverson wrote: Hello, sedm1000 wrote: Sorry - I figured that this to be a more common defined error than anything specific to the data/function... Thanks for looking at this. The data and function are below. Creating a single line of the data.frame at a time will work (i.e. fold(s)) For multiple line data.frames, an error is generated. Ideally I would like to record the output from fold(sq) in a two column data.frame, whether it requires reading in the data to fold one line at a time or in bulk. library(GeneRfold) s- ATTATGCATCGACTAGCATCACTAG fold(s) [[1]] [1] ..... [[2]] [1] -2.3 sq - data.frame(c(ATGTGTGATATGCATGTACAGCATCGAC, + ACTAGCACTAGCATCAGCTGTAGATAGA, + ACTAGCATCGACATCATCGACATGATAG, + CATCGACTACGACTACGTAGATAGATAG, + ATCAGCACTACGACACATAGATAGAATA)) fold(sq) Building on Erik's comments, perhaps trying: sq - data.frame(s1 = c(ATGTGTGATATGCATGTACAGCATCGAC, + ACTAGCACTAGCATCAGCTGTAGATAGA, + ACTAGCATCGACATCATCGACATGATAG, + CATCGACTACGACTACGTAGATAGATAG, + ATCAGCACTACGACACATAGATAGAATA), stringsAsFactors=FALSE) stringsAsFactors=FALSE leaves the character vector unfactored. str(sq) 'data.frame': 5 obs. of 1 variable: $ s1: chr ATGTGTGATATGCATGTACAGCATCGAC ACTAGCACTAGCATCAGCTGTAGATAGA ACTAGCATCGACATCATCGACATGATAG CATCGACTACGACTACGTAGATAGATAG ... Passing sq would still be passing a list. You probably want just the first and only column. str(sq$s1) chr [1:5] ATGTGTGATATGCATGTACAGCATCGAC ACTAGCACTAGCATCAGCTGTAGATAGA ... fold(sq$s1) # passing a character vector, which is what the error message says is needed. -- David. Error in fold(sq) : STRING_ELT() can only be applied to a 'character vector', not a 'list' struct - t(as.data.frame(sapply(sq[,1], fold, t=37))) Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer' This appears to be a Bioconductor package, so if this doesn't help, I'd ask on the specific bioconductor mailing list. I don't have the package installed, so take the following advice with that in mind. Did you look at the str(sq) ? It is not a character vector, it is a factor, so you might need to convert or see stringsAsFactors in ? options. Try lapply(sq[, 1], function(x) fold(as.character(x))) If that doesn't work, try the other list. Good luck, Erik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer'
Thanks for your time with this. Erik's solution works best to deal with the input... I'll try to reshape the output back into the appropriate columns. David, fold(sq$s1) only outputs the result for the first sequence in the list I'm afraid. The 'fold' function doesn't deal well with spaces... Thanks again. -- View this message in context: http://r.789695.n4.nabble.com/Error-in-FUN-X-1L-STRING-ELT-can-only-be-applied-to-a-character-vector-not-a-integer-tp2226811p2228157.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer'
Hello, PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. We don't know the function you're using or the data you applied the function to, which makes it almost impossible to help. Can you use ?dput to output the data.frame you're experiencing trouble with, and the function definition you're using to give us a reproducible, self-contained example? sedm1000 wrote: I am receiving this error running a command on a multi-row data-frame. The data is strings of text (each with new line separator, no spaces, no numerical characters). Error in FUN(X[[1L]], ...) : STRING_ELT() can only be applied to a 'character vector', not a 'integer' I can run single text string into the same command, and so the issue seems to be how the package deals with the second row - but I can't work out quite where the deficit is. If anybody has spotted this error before, and knows how to resolve it, that would be much appreciated. Cheers. R version 2.11.0 (2010-04-22) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GeneRfold_1.6.0 GeneR_2.18.0 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
