How to load the new dataset and gene-sets into singscore package in R
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vikram56j • 0
@vikram56j-22209
Last seen 4.7 years ago

I have performed the singscore package in R with example script. Can i know the data format to input new dataset and gene-sets in the singscore in R and perform the analysis

software error • 1.1k views
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Cross-posted on Biostars: https://www.biostars.org/p/404637/

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@bhuvad-17623
Last seen 11 days ago
Australia

Hi,

I know it is late but for future users, the input formats are as such:

expression data: matrix, data.frame, DGEList, SummarizedExperiment, Matrix (all with genes along the rows and samples along the columns) gene set: character list, GeneSet object from the GSEABase package (make sure gene ids match with those in the expression data)

We have also created a detailed workflow to demonstrate how you can use singscore to process TCGA data using signatures from the molecular signatures database (MSigDB) F1000Research workflow. This workflow is also available in the SingscoreAMLMutations R/Bioconductor workflow package (with a Chinese translation).

Cheers, Dharmesh

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