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
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'.