Question

How to render summary list for `GRangesList` by using `SummarizedExperiment` package?

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Jurat Shahidin ▴ 80

@jurat-shahidin-9488

Last seen 4.7 years ago

Chicago, IL, USA

Hi:

Given processed ChIP-Seq peaks in `GRangesList`, I want to use the functions from `SummarizedExperiment` package to render succinct summary output. However, I looked into package vignette and tried to learn how to use this on `GRangesList`. My goal is, based on `GRangesList`, I want to let R print me out the short summary list (# of regions, metadata column, rows/columns, and others). I learned the features of `SummarizedExperiment` from package vignette how to do it, but I got an error. Here is my attempt:

lapply(seq_along(grs), function(x) {
    SummarizedExperiment(assays = NROW(x),
                         rowRanges = x,
                         colData=mcols(x))
})

the error message is:

Error in if (assays_nrow != rowData_nrow) { : argument is of length zero

why getting this error? How to fix that? How to apply `summarizedExperiment` method on `GRangesList` to render summary list? Can anyone direct me how to make this happen? Thanks in advance

r summarizedexperiment grangeslist • 1.9k views

ADD COMMENT • link 7.7 years ago Jurat Shahidin ▴ 80

1

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Briefly, there is no simple approach to this. However, to get a working example:

library(GenomicRanges)

library(SummarizedExperiment)

example(GRangesList) # creates 'grl' in .GlobalEnv

colrep = function(x,n) matrix(x, nr=length(x), nc=n) # utility to create usable 'assay'

msel = lapply(grl, function(x) SummarizedExperiment(colrep(start(x),nrow(mcols(x))), rowRanges=x,

colData=mcols(x)))

> msel

$gr1

dim: 1 1

metadata(0):

assays(1): ''

rownames: NULL

rowData names(2): score GC

colnames: NULL

colData names(2): score GC

$gr2

dim: 2 2

metadata(0):

assays(1): ''

rownames: NULL

rowData names(2): score GC

colnames: NULL

colData names(2): score GC

$gr3

dim: 2 2

metadata(0):

assays(1): ''

rownames: NULL

rowData names(2): score GC

colnames: NULL

colData names(2): score GC

Your attempt failed because you did not supply a matrix for "assay".

ADD REPLY • link 7.7 years ago Vincent J. Carey, Jr. 6.7k

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@Vincent: Dear Vincent, thanks for your help. BTW, I am expecting rather simple, intuitive solution to achieve my goal. What if I first flatten out GRangesList as one common GRanges, then use SummarizedExperiment package to render simple statistics? Is that workable?

ADD REPLY • link 7.7 years ago Jurat Shahidin ▴ 80

1

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I don't know that SummarizedExperiment is a good target for what you are trying to do. Is there a matrix of values to serve as "assay", with rows corresponding to features and columns corresponding to samples? Organizing such a matrix in coordination with feature-level and sample-level and experiment-level metadata is the primary purpose of SummarizedExperiment. The terminology likely derives from the common use case of summarizing short reads from multiple samples into a matrix, with the primary "summary" step being the quantification of 'features' through operations on sample-specific collections of reads. I am not sure this is what you are trying to do given the brevity of your description of intent. On Sun, Mar 12, 2017 at 9:49 AM, Jurat Shahidin [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Jurat Shahidin <https: support.bioconductor.org="" u="" 9488=""/> wrote Comment: > How to render summary list for `GRangesList` by using > `SummarizedExperiment` package? > <https: support.bioconductor.org="" p="" 93740="" #93743="">: > > @Vincent: Dear Vincent, thanks for your help. I am wondering any easier > workaround to do this. I am expecting rather simple, intuitive solution to > achieve my goal. What if I first flatten out `GRangesList` as one common > `GRanges`, then use `SummarizedExperiment` package to render simple > statistics? Is that workable? > > ------------------------------ > > Post tags: r, summarizedexperiment, grangeslist > > You may reply via email or visit https://support.bioconductor. > org/p/93740/#93743 >

ADD REPLY • link 7.7 years ago Vincent J. Carey, Jr. 6.7k

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@Vincent: Dear vincent, the problem I faced is printing out GRangesList is not favorable for me, while rendering summary of each GRanges would be good option aims to give clear output for the user, that's why I am trying to find the easy workaround for this problem. Hope you will direct me some useful solution. Thanks in advance :)

ADD REPLY • link 7.7 years ago Jurat Shahidin ▴ 80