Converstion of Ranged Summarized Experiment to Data Frame
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sylvie2 • 0
@sylvie2-24355
Last seen 22 months ago

Hi,

Is it possible to convert a Ranged Summarized Experiment into a Matrix or a Data Frame. If so can you provide a script to do so?

Thanks!

SummarizedExperiment RangedSummarizedExperiment • 597 views
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svlachavas ▴ 800
@svlachavas-7225
Last seen 22 days ago
Germany/Heidelberg/German Cancer Resear…

Dear Sylvie,

could you provide more details about the data type that you analyze, and your goal ? Generally the scope of this group is not just to provide scripts, rather to assist in specific tasks and technical-methodological questions regarding R packages and Bioconductor-

based on your question, initially you can read in the detail the R package RaggedExperiment:

http://bioconductor.org/packages/release/bioc/vignettes/RaggedExperiment/inst/doc/RaggedExperiment.html#7*assayfunctions

where it provides various functions to represent ranged data into a resulting matrix-

more directly, you could use the function assay as illustrated below or directly type ?RangedSummarizedExperiment:

nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                     IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                     strand=sample(c("+", "-"), 200, TRUE),
                     feature_id=sprintf("ID%03d", 1:200))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                     row.names=LETTERS[1:6])
rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
                     rowRanges=rowRanges, colData=colData)

xx <- assay(rse)
head(xx)
            A        B        C         D         E        F
[1,] 3412.971 9201.326 8040.690 5732.4395 1662.0214 1865.154
[2,] 4691.457 8856.418 5962.201 3237.7014 3872.6439 6712.661
[3,] 4542.271 7572.359 9178.876 4994.8515 8413.9258 2322.053
[4,] 7670.194 3332.390 5971.705 9894.6457 5655.6748 5615.336
[5,] 8056.919 2571.537 1035.424  374.3122 5812.4404 2452.022
[6,] 2013.136 1619.997 9314.377 3784.2708  654.1187 2885.155

Hope that helps,

Efstathios

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Dear Efstathios,

I'm working with single cell ATAC datasets. I was trying to generate a heatmap showing accessibiltiy to transcription factor motif sequences by calling geneAccessibility() and heatmapGeneAccessibility from ATACCoGAPS both command lines from the latter.

However I was getting error messages owing to the fact that I was working with RangedSummarizedExperiment rather that a dataframe. Hence my need for a workaround.

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Dear Sylvie,

I have never worked with single cell ATAC analysis-however, I think it would be much more helpful, instead of giving general descriptions, to either modify your post, or create a new one, including some example code that lead to your error, along with your sessionInfo. Additionally, you should tag also the responsive R packages that included the relative functions. Then, more people could comment or provide suggestions about your errors.

Efstathios

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