Error while smoothing BS-seq data with bsseq
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@andreucat91-8929
Last seen 4.8 years ago
Spain

I have a problem when I try to smooth my data with the package bsseq. This data comes from bismark and has been previously loaded to R with read.bismark function without problems. You have the commands I used below:

library("bsseq")
files_chh = list.files(path = ".", pattern = "CHH")
meth <- read.bismark(files_chh, c("P150_1","P150_2","P150_3","P60_1","P60_2","P60_3","PM1","PM2","PM3"))
splitBtSample <- list()
for (x in 1:ncol(meth)) {
  splitBtSample[x] <- BSmooth(meth[,x], mc.cores = 5, verbose = TRUE)
}
[BSmooth] preprocessing ... done in 154.6 sec
[BSmooth] smoothing by 'sample' (mc.cores = 5, mc.preschedule = FALSE)
[BSmooth] smoothing done in 338.3 sec
Error in `colnames<-`(`*tmp*`, value = "P150_1") :
  attempt to set 'colnames' on an object with less than two dimensions

As you can see, an error appears and I am not able to find the origin. Do you have any idea what is going on? I have analysed other data following these commands and all went fine. Raw files seem to be OK.

By the way, do you recommend filtering the data by setting a coverage threshold? How would you do that?

Thank you very much.

bsseq • 1.1k views
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@kasper-daniel-hansen-2979
Last seen 11 weeks ago
United States
Don't you need double brackets on your splitbySample[x]? But really BSmooth is set up to do what you want, you should just have to do meth = BSmooth(meth, parallelBy = "sample", mc.cores = 5 ) The coverage threshold depends a little on your experiment and the obtained coverage. I have tended to increase my threshold over the last couple of years as depth has gotten bigger, but that is based on trying to be more conservative when I can afford it. Best, Kasper Best, Kasper On Mon, Oct 5, 2015 at 11:56 AM, andreucat91 [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User andreucat91 <https: support.bioconductor.org="" u="" 8929=""/> wrote Question: > Error while smoothing BS-seq data with bsseq > <https: support.bioconductor.org="" p="" 72961=""/>: > > I have a problem when I try to smooth my data with the package *bsseq*. > This data comes from bismark and has been previously loaded to R with > *read.bismark* function without problems. You have the commands I used > below: > > library("bsseq") > files_chh = list.files(path = ".", pattern = "CHH") > meth <- read.bismark(files_chh, c("P150_1","P150_2","P150_3","P60_1","P60_2","P60_3","PM1","PM2","PM3")) > splitBtSample <- list() > for (x in 1:ncol(meth)) { > splitBtSample[x] <- BSmooth(meth[,x], mc.cores = 5, verbose = TRUE) > } > [BSmooth] preprocessing ... done in 154.6 sec > [BSmooth] smoothing by 'sample' (mc.cores = 5, mc.preschedule = FALSE) > [BSmooth] smoothing done in 338.3 sec*Error in `colnames<-`(`*tmp*`, value = "P150_1") : > attempt to set 'colnames' on an object with less than two dimensions* > > As you can see, an error appears and I am not able to find the origin. > > By the way, do you recommend filtering the data by setting a coverage > threshold? How would you do that? > > > > ------------------------------ > > Post tags: bsseq > > You may reply via email or visit Error while smoothing BS-seq data with bsseq >
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@nikolayoskolkov-12968
Last seen 4.4 years ago

Hi Kasper,

I have a similar error from BSmooth that I can not solve:

bismarkBSseq.fit<-BSmooth(bismarkBSseq,mc.cores=1,verbose=TRUE)
[BSmooth] preprocessing ... done in 35.6 sec
[BSmooth] smoothing by 'sample' (mc.cores = 1, mc.preschedule = FALSE)
[BSmooth] smoothing done in 2893.2 sec
Error in `colnames<-`(`*tmp*`, value = c("10D", "21D", "22D", "28D")) :
  attempt to set 'colnames' on an object with less than two dimensions

The BSseq object was prepared in the following way

bismarkBSseq<-read.bismark(files=c("10D_S2_001_bismark_bt2_pe.deduplicated.bismark.cov.gz","21D_S3_001_bismark_bt2_pe.deduplicated.bismark.cov.gz","22D_S4_001_bismark_bt2_pe.deduplicated.bismark.cov.gz","28D_S1_001_bismark_bt2_pe.deduplicated.bismark.cov.gz"),sampleNames=c("10D","21D","22D","28D"),rmZeroCov=TRUE,strandCollapse=FALSE,fileType="cov",mc.cores=1,verbose=TRUE)

What can be wrong with BSmooth?

Best,

Nikolay

 

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@nikolayoskolkov-12968
Last seen 4.4 years ago

And here btw is the BSseq object structure:

  ..@ trans          :function ()  

  ..@ parameters     : list()
  ..@ rowRanges      :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
  .. .. ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. .. .. ..@ values         : Factor w/ 191 levels "1","9","20","2",..: 1 2 3 4 5 6 7 8 9 10 ...
  .. .. .. .. ..@ lengths        : int [1:191] 4666694 2402572 1527595 4333907 2652774 1725135 2922224 1178 1652754 1185586 ...
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. .. .. ..@ start          : int [1:56822515] 10469 10470 10471 10472 10484 10485 10489 10490 10493 10494 ...
  .. .. .. .. ..@ width          : int [1:56822515] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. ..@ NAMES          : NULL
  .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ strand         :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 3
  .. .. .. .. ..@ lengths        : int 56822515
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. ..@ nrows          : int 56822515
  .. .. .. .. ..@ listData       : Named list()
  .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
  .. .. .. .. ..@ seqnames   : chr [1:191] "1" "9" "20" "2" ...
  .. .. .. .. ..@ seqlengths : int [1:191] NA NA NA NA NA NA NA NA NA NA ...
  .. .. .. .. ..@ is_circular: logi [1:191] NA NA NA NA NA NA ...
  .. .. .. .. ..@ genome     : chr [1:191] NA NA NA NA ...
  .. .. ..@ metadata       : list()
  ..@ colData        :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : chr [1:4] "10D" "21D" "22D" "28D"
  .. .. ..@ nrows          : int 4
  .. .. ..@ listData       : Named list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ assays         :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field
  .. ..$ data: NULL
  .. ..and 14 methods.
  ..@ NAMES          : NULL

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Hi Nikolay,

Did you figure out how to solve this problem?

I got the same situation and I don't know what to do.

Thank you,

Kai

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