Question

How to count gene expression level in R?

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3.3 years ago

ja4123 ▴ 30

Hi! Could anyone suggest some reasonable quick way (library or tutorial) to get table with gene expression level with data listed below?

.tsv with barcodes

.tsv with genes

and .mtx matrix

I am new in this and I will appreciate any help.

expression seurat r gene bioconductor • 2.9k views

ADD COMMENT • link 3.3 years ago by ja4123 ▴ 30

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Come on. How can anyone help if you don't say what format your data is now?

ADD REPLY • link 3.3 years ago by swbarnes2 14k

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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?

ADD REPLY • link 3.3 years ago by cpad0112 21k

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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

ADD REPLY • link 3.3 years ago by ja4123 ▴ 30

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"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

ADD REPLY • link 3.3 years ago by cpad0112 21k

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Thanks very much for help. I will try those links.

ADD REPLY • link 3.3 years ago by ja4123 ▴ 30

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Anyway, what do you think about solution in [SOLVED] How to build a table with gene expression per cell type with Seurat ? ?

ADD REPLY • link 3.3 years ago by ja4123 ▴ 30

score 1 · Answer 1 · 2021-09-04

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3.3 years ago

ATpoint 86k

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.

ADD COMMENT • link 3.3 years ago by ATpoint 86k

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Do you know way to store that count matrix in .tsv or .csv file? Sorry for not smart question but R in not my strong site. I am definitely prefer python.

ADD REPLY • link 3.3 years ago by ja4123 ▴ 30

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You can export any matrix in R with write.table() but depending on the dimensions it is going to be large, that is why these sparse formats exist.

ADD REPLY • link 3.3 years ago by ATpoint 86k

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Should I count that matrix after normalization, feature selection, scaling and dimensional reduction? Or wheres before?

ADD REPLY • link 3.3 years ago by ja4123 ▴ 30

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Count? what does that mean?

ADD REPLY • link 3.3 years ago by ATpoint 86k

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I need to get table with gene expression level (count matrix). I did not confuse the concepts?

ADD REPLY • link 3.3 years ago by ja4123 ▴ 30

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That would be the mtx file after reading into R with readMM, but if you prefer python then I am sure there are ways to read it into python. mtx is short for MatrixMarket, google will for sure give suitable packages for python to read it.