Question: Getting a count matrix from a SummerizedExpriment with EasyRNASeq
0
gravatar for Sylvain Foisy
4.8 years ago by
Canada
Sylvain Foisy30 wrote:

Hi,

I previously used EasyRNASeq 1.8 to get count matrices from BAM files with a simple write.table command. I am trying to move to v. 2.0.8 but I just can’t seem to be able to do the same with the SummerizedExperiment object created…  I know that I could create object sot feed directly to edgeR or deseq2 but we want to do our own analysis with various other techniques.

Probably a trivial thing but I am no R/Bioconductor wizard ;-)

Thanks in advance

Sylvain

easyrnaseq • 1.1k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Sylvain Foisy30
Answer: Getting a count matrix from a SummerizedExpriment with EasyRNASeq
1
gravatar for Sylvain Foisy
4.8 years ago by
Canada
Sylvain Foisy30 wrote:

 

Hi Andrzej,

It does not provide meaningful info:

> ?SummarizedExperiment

No documentation for ‘SummarizedExperiment’ in specified packages and libraries:

you could try ‘??SummarizedExperiment’

> ??SummarizedExperiment

Help files with alias or concept or title matching

‘SummarizedExperiment’ using fuzzy matching:

easyRNASeq::BamFileList

                        Count summarization and normalization pipeline

                        for Next Generation Sequencing data.

biovizBase::mold        mold data into data.frame

DESeq2::collapseReplicates

                        Collapse replicates in a SummarizedExperiment

                        or DESeqDataSet

GenomicRanges::SummarizedExperiment-class

                        SummarizedExperiment instances

Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for

entries like 'PKG::FOO-TYPE'.

 

What's next?

S

ADD COMMENTlink written 4.8 years ago by Sylvain Foisy30
library(GenomicRanges)
?SummarizedExperiment
ADD REPLYlink written 4.8 years ago by James W. MacDonald50k

Hi James,

Thanks for the input; I would have thought that loading easyRNASeq would have also loaded GenomicRanges... I'll insert the statement in my code.

S

 

ADD REPLYlink written 4.8 years ago by Sylvain Foisy30

easyRNASeq imports all the functions it needs from GenomicRanges, but doesn't depend on that package (e.g., it won't load it by default).

ADD REPLYlink written 4.8 years ago by James W. MacDonald50k
Answer: Getting a count matrix from a SummerizedExpriment with EasyRNASeq
0
gravatar for Andrzej Oleś
4.8 years ago by
Andrzej Oleś720
Heidelberg, Germany
Andrzej Oleś720 wrote:

Hi Sylvain,

you can use the assays method to extract the count table from your SummerizedExperiment object, for details see ?SummarizedExperiment.

Best,

Andrzej

ADD COMMENTlink written 4.8 years ago by Andrzej Oleś720
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