Question: Chipseeker : problem running Chipseeker to ENCODE datasets
0
gravatar for snigdhapola
4.6 years ago by
CRRao AIMSCS, India
snigdhapola0 wrote:

Hi,

I am trying to run ChiPseeker  for ENCODE datasets and been getting the following error:

"Error in unlist(metadata(TXDB)) :
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection"

 

The code I have been running is:

> files=read.table("epiGenomeEncodeFiles")
> files=as.vector(files[,1])
>
> peakAn=function(x = files){
+ library(ChIPseeker)
+ library(org.Hs.eg.db)
+ library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+
+ getGenomicAnnoStat <- function(peakAnno) {
+     if ( class(peakAnno) == "GRanges" )
+         peakAnno <- as.data.frame(peakAnno)
+     anno <- peakAnno$annotation
+     anno <- sub(" \\(.+", "", anno)
+
+     ## count frequency
+     anno.table <- table(anno)
+
+     ## calculate ratio
+     anno.ratio <- anno.table/ sum(anno.table) * 100
+     anno.df <- as.data.frame(anno.ratio)
+     colnames(anno.df) <- c("Feature", "Frequency")
+     return(anno.df)
+ }
+
+
+ annotatedPeak <- annotatePeak(x, tssRegion = c(-4000, 4000), TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene, annoDb = "org.Hs.eg.db")
+
+ outF = gsub("Peak4_4", ".CSpeaks", x)
+ write.table(as.data.frame(annotatedPeak), file=outF, sep="\t")
+ }
>
> data1=lapply(files, peakAn)

Please suggest if the error am getting is due to the difference in the format of input files (ENCODE files), I am trying to run the code for , or it is an issue with annotatedPeak function. Any suggestions in this regard would be helpful.

Thanks,

Snigdha.

 

chipseeker • 1.2k views
ADD COMMENTlink modified 4.6 years ago by Guangchuang Yu1.1k • written 4.6 years ago by snigdhapola0
Answer: Chipseeker : problem running Chipseeker to ENCODE datasets
0
gravatar for Guangchuang Yu
4.6 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

Can you post the link to download this ENCODE data? So that I can check this issue.

 

Bests,

Guangchuang

ADD COMMENTlink written 4.6 years ago by Guangchuang Yu1.1k
Answer: Chipseeker : problem running Chipseeker to ENCODE datasets
0
gravatar for snigdhapola
4.6 years ago by
CRRao AIMSCS, India
snigdhapola0 wrote:

Hi,

Thank you for the response. We were trying to run it with developmental version of R and was encountering the error, even for the example data provided with the package. We tried it with R 3.2.0 and it is running fine. Thanks again for the response.

ADD COMMENTlink written 4.6 years ago by snigdhapola0
Answer: Chipseeker : problem running Chipseeker to ENCODE datasets
0
gravatar for Guangchuang Yu
4.6 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

The examples in devel branch of ChIPseeker has no problem, as the vignette was generated correctly, see http://www.bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

 

ADD COMMENTlink written 4.6 years ago by Guangchuang Yu1.1k
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