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
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West Hartford, CT
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