Data structure for my dataset
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Sim1pall8a • 0
@sim1pall8a-12948
Last seen 5.2 years ago

Hi, I'm new at R/Bioconductor.

I need a data structure that represent the dataset that i'm working with.

My dataset is a set of samples: each sample is made up of two file (.gdm or .gtf)

1) set of region:

chr     left       right   strand name score signal    pvalue    qvalue  peak

chr1    237680    237830    *    .    0    17.1875    15.9472    -1    -1
chr1    521500    521650    *    .    0    15.5625    18.0962    -1    -1
chr1    714060    714210    *    .    0    139.40625  316.755    -1    -1

assay    DNase-seq
assembly    hg19
audit_internal_action    experiment not submitted to GEO, out of date analysis
biological_replicate(s)    2
biosample_life_stage    unknown
biosample_organism    Homo sapiens

(these example are taken from my files)

I know Granges and GrangesList are useful for representing a regions or list of regions respectively, but i don't know how to represent and bind my metadata to my regions.

is there any other package/class that could help me or I need to create one "ad hoc"?

metadata grangeslist granges sample • 655 views
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@michael-lawrence-3846
Last seen 8 months ago
United States

I think you could just store the metadata in a list as the metadata() component of the GRanges.

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thanks, but in this way it create as many columns as the different value in my metadata and replicate the same value for every rows and this is not what i want.

and also I use metadata in GRanges for extra column of my region not cover in GRanges (name score signal    pvalue    qvalue  peak)

I would like something similar to metadata in summarizedExperiment package

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metadata() on GRanges is the same as metadata() on SummarizedExperiment. Maybe you are getting confused with mcols()?

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yes, I was confused :) , I didn't understand completely metadata in summarizedExperiment

I think i got it, thanks!