I have an unusual question: I am working on a Erasmus internship project with Drosophila mutants at 2 different timepoints and with WT, KO and KI condition. A company analyzed the data using DESeq2 and I have only got loads of PDFs and the results_apeglm.xlsx file.
This contains: Transcripts per million for each gene, replicate and timepoint with the comparison for looking at DEGs - so I have a padj and log2FC value. A snippet is attached as an example.
I now want to construct a graph and clustering where genes that are going in changing directions between WT and KO over time become visible out of the hundreds of candidate DEGs. With this I want to narrow down the long list to make it verifiable with qPCR and serve as a marker for transformation from presymptomatic to symptomatic.
I am setting up my analysis in R and want to use the degPatterns() function from DEGReport, as it gives a nice visual output and clusters the genes for me.
How can I now transform my Excel sheets, to a matrix format that I can use with degPatterns()? The example with the Summarized Experiment given in the vignette is not really helpful to me, sadly.
Thank you all for reading, pondering and helping with my question! I would be very happy if there´s a way to solve my data wrangling issue.
All the best,
Paul
Hi, what exactly do you need? A matrix from excel sheet. Then, simply read excel file using
as.matrix(readxl::read_excel(your_file_location))
function. You need to remove few columns and then matched the columns to meta data.
and IF degPatterns() function is not working properly, then you may need to clean and re-transform your data.
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