How to count gene expression level in R?
1 answer
Making scRNA counts file from barcodes, genes and matrix.mtx file
The mtx file stores the counts, the barcodes are the colnames and the genes are the rownames.
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Come on. How can anyone help if you don't say what format your data is now?
You would need phenotype data in addition to gene and matrix. In addition, please pose if gene order (in from genes .tsv) match with order of values (in matrix). Matrix needs sample names. Do you have corresponding sample names matching with matrix columns?
I found this post: [SOLVED] How to build a table with gene expression per cell type with Seurat ?. This seems to be what I want, but I was wondering if the whole thing could be done in R.
btw. thx for the answer
"The context of "I used CellRanger from 10X genomics..." would be needed for most people to provide you with actual help..." Devon Ryan 's comment relevant even after 3.1 yr :).
Here is the tutorial on how to load the scdata in R: https://hbctraining.github.io/scRNA-seq/lessons/readMM_loadData.html. 10x it self has put manual over there how to do this in R and python: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices
Thanks very much for help. I will try those links.
Anyway, what do you think about solution in [SOLVED] How to build a table with gene expression per cell type with Seurat ? ?