Question: How to subset S4 list with 5 Granges elements
0
gravatar for khani.sajjad
8 months ago by
khani.sajjad0 wrote:

I have a S4 list (peakAnnoList) which contains many Chip-Seq data in the Granges format.

I would like to subset/filter peakAnnoList based on one of its slot ($width > 4000). Here is the code to generate peakAnnoList:

  ## loading packages
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
library(clusterProfiler)

files <- getSampleFiles()
peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb,
                       tssRegion=c(-3000, 3000), verbose=FALSE)

peakAnnoList is a list with 5 elements and each elements contains combination of "csAnno" and "GRanges" and some other objects. I would like to filter all 5 elements of peakAnnoList for width > 4000. Here is the position of width (peakAnnoList[[1]]@anno@ranges@width). I can do that with only 1 elements of list by converting it to data.frame, but I would like to have it for all the elements.

chip-seq • 295 views
ADD COMMENTlink modified 8 months ago by RamRS24k • written 8 months ago by khani.sajjad0

It's the problem of R dataframe and file handling. Please tag R, data.frame and related tags. Also, please provide the file sample from which you want to extract the data. Without knowing S4 list structure it's hard to imagine the solution.

ADD REPLYlink written 8 months ago by kashiff007100
0
gravatar for RamRS
8 months ago by
RamRS24k
Houston, TX
RamRS24k wrote:

You should look into apply family of functions, especially lapply. Given that peakAnnoList is a list, you should be able to

filteredItems <- lapply(peakAnnoList, 
                            function(item) {
                                if(item@anno@ranges@width > 4000)
                                    return(item)
                            }
                        );
ADD COMMENTlink modified 8 months ago • written 8 months ago by RamRS24k
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