Question: Problem with prettyPrint (Chimera)
0
gravatar for anders
2.5 years ago by
anders0
anders0 wrote:

I used the STAR example and I am getting the follow error: Error in `dimnames<-.data.frame`(`*tmp*`, value = list(c("gene1", "chr.gene1",  :
  invalid 'dimnames' given for data frame

With the example "mcf7.FMFusionReport" from fusionmap it is working.

> download.file("https://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download", "Chimeric.out.junction.zip", mode="wb")
trying URL 'https://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download'
Content type 'application/octet-stream' length 26413272 bytes (25.2 MB)
==================================================
downloaded 25.2 MB

> unzip("Chimeric.out.junction.zip")
> tmp <- importFusionData("star", "Chimeric.out.junction", org="hg19", min.support=100)

chrM is removed from fusion acceptor

chrM is removed from fusion donor

Importing 73 fusions
'select()' returned 1:1 mapping between keys and columns

.........................................................................
> prettyPrint(tmp, "test2.txt", fusion.reads="spanning")Error in `dimnames<-.data.frame`(`*tmp*`, value = list(c("gene1", "chr.gene1",  :
  invalid 'dimnames' given for data frame

 

Any help will be really appreciated!

 

 

chimera prettyprint • 511 views
ADD COMMENTlink modified 2.1 years ago by mrp0 • written 2.5 years ago by anders0
Answer: Problem with prettyPrint (Chimera)
1
gravatar for raffaele calogero
2.5 years ago by
Italy/Turin/University of Torino
raffaele calogero500 wrote:
Hi Anders, I will check the problem on thenext days Cheers Ra Prof. Raffaele A Calogero Tel +39 3333827080 Email raffaele.calogero@unito.it raffaele.calogero@gmail.com Sent from my iPhone On 27 Feb 2017, at 14:18, anders [bioc] <noreply@bioconductor.org> wrote: Activity on a post you are following on support.bioconductor.org User anders <https: support.bioconductor.org="" u="" 12456=""/> wrote Question: Problem with prettyPrint (Chimera) <https: support.bioconductor.org="" p="" 93112=""/>: I used the STAR example and I am getting the follow error: Error in `dimnames<-.data.frame`(`*tmp*`, value = list(c("gene1", "chr.gene1", : invalid 'dimnames' given for data frame With the example "mcf7.FMFusionReport" from fusionmap it is working. > download.file("https://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download", "Chimeric.out.junction.zip", mode="wb") trying URL 'https://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download' Content type 'application/octet-stream' length 26413272 bytes (25.2 MB) ================================================== downloaded 25.2 MB > unzip("Chimeric.out.junction.zip") > tmp <- importFusionData("star", "Chimeric.out.junction", org="hg19", min.support=100) chrM is removed from fusion acceptor chrM is removed from fusion donor Importing 73 fusions 'select()' returned 1:1 mapping between keys and columns ......................................................................... > prettyPrint(tmp, "test2.txt", fusion.reads="spanning")Error in `dimnames<-.data.frame`(`*tmp*`, value = list(c("gene1", "chr.gene1", : invalid 'dimnames' given for data frame Any help will be really appreciated! ------------------------------ Post tags: prettyPrint, Chimera You may reply via email or visit Problem with prettyPrint (Chimera)
ADD COMMENTlink written 2.5 years ago by raffaele calogero500
Answer: Problem with prettyPrint (Chimera)
0
gravatar for mrp
2.1 years ago by
mrp0
USA
mrp0 wrote:

Hello Raffaele, 

 

I was wondering if there is a solution yet to the problem mentioned in this thread? I am facing the same problem and getting the following error on using the prettyprint function:

Error in `dimnames<-.data.frame`(`*tmp*`, value = list(c("gene1", "chr.gene1",  : 
  invalid 'dimnames' given for data frame

 

these were my command lines:

temp <- importFusionData("star", "filename.Chimeric.out.junction", org = "hg38", min.support = 10)

prettyPrint(temp, "temp.df.txt", fusion.reads = "spanning")

 

 

Any help on this will be highly appreciated. thanks!

ADD COMMENTlink written 2.1 years ago by mrp0
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