Cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame error.

Question

[Aishwarya.Kulkarni]

Hi,

I am trying to output a result of matchPWM and I get the following error when I try to output it using write command:

write(as.data.frame(data), "chr9_RBPJ_R.txt", sep="\n")
cannot coerce class 'structure("IRanges", package = "IRanges")' into a data.frame

where data is

data<-list(hits = as(hits, "IRanges"), scores = scores)

hits=results of matchPWM and scores are the scores for each hit.

here is the sessioninfo

> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.26.1
[3] GenomicRanges_1.10.7               Biostrings_2.26.3
[5] IRanges_1.16.6                     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] parallel_2.15.3 stats4_2.15.3   tools_2.15.3

Thanks in advance

[Devon Ryan]

Why would you expect there to be a coercion method for a custom structure?

[Aishwarya.Kulkarni]

ok, if that's the case then how do I output the structure into a file?

[Devon Ryan]

help(save)

[Aishwarya.Kulkarni]

I did try saving it with save , however it gives me a gibberish output in the file.

[Devon Ryan]

The results from save() aren't meant to be human readable. If you want this written to a text file then you'll need to either write a method to convert it to a type that can be directly written as text or write your own method to write it in some convenient text format.

[insilico123]

cat(data, file="Report.out")

[insilico123]

save() is meant for saving your current workspace which can be read back from the file at a later date by using the function load. It is not for printing the output to a file

[Devon Ryan]

save() can save individual objects, not just the workspace.

[insilico123]

Ya individual objects can be saved, but it can be retrieved to the workspace by load() method. But here she wants to print the data to a file, not for loading the data to the workspace.

[Aishwarya.Kulkarni]

Thanks a lot!

[Aishwarya.Kulkarni]

when I give the command, it gives me an error

cat(hits, file="ABC.txt")
Error in cat(list(...), file, sep, fill, labels, append) : 
  argument 1 (type 'S4') cannot be handled by 'cat'
> class(hits)
[1] "XStringViews"
attr(,"package")
[1] "Biostrings"

[komal.rathi]

Are you trying to write the pair wise alignments to a file? Can you give some code to show your data & what functions you used? Some reproducible example?

[Aishwarya.Kulkarni]

Hi I am using matchPWM a function to scan a position weight matrix on and sequence to get the hits, and I am trying to output these hits into a file.

[insilico123]

You can use sink

It can output any variable into a file including XStringViews

[komal.rathi]

Ok it is still difficult to debug your problem without a reproducible example but anyway, does your "data" object look like this:

  start      end width
    [1]       96      103     8 [ATAAACAT]
    [2]      264      271     8 [GTAAGCAG]
    [3]      317      324     8 [GCAAACAA]
    [4]      488      495     8 [GTAAAGAG]
    [5]     1400     1407     8 [GGAAACAC]

And do you want to write this entire set to a file or just the matched sequences given within the square brackets?

[Aishwarya.Kulkarni]

Yes exactly!

[insilico123]

then you can sink subject(hits) to a file

[Aishwarya.Kulkarni]

I didn't quiet understand, do you mean cat(hits, file="ABC.txt")?

[insilico123]

Use it to save the hits

sink("ABC.txt")
hits
sink()

[insilico123]

Give some code to show your data, or you can try use sink

sink("ABC.txt")
hits
sink()

Answer 1

[komal.rathi]

Okay, so this may be not the best method but works,

> class(dat)
[1] "XStringViews"
attr(,"package")
[1] "Biostrings"
> x <- data.frame(start=start(dat),end=end(dat),width=width(dat),as(dat,"XStringSet"))

x is a data.frame object and you can write it to a file like you'd normally do.

Update: Aishwarya.Kulkarni I have edited my code to make it faster. Give it a try.

Answer 2

[brentp]

You can use as.data.frame on a GRanges object and it can have your scores attached, so:

library(GenomicRanges)

scores = c("good", "better", "best")
g = GRanges(seqnames=c("1", "2", "3"), ranges=IRanges(start=c(100, 200, 300), width=20))

values(g) = scores
print(as.data.frame(g))

Outputs:

  seqnames start end width strand  value
1        1   100 119    20      *   good
2        2   200 219    20      * better
3        3   300 319    20      *   best