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tanaylab / metacell

Metacell - Single-cell mRNA Analysis
https://tanaylab.github.io/metacell
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Gene quantification in metacells #40

Closed nessa0389 closed 3 years ago

nessa0389 commented 4 years ago

How to find out the quantity of a particular gene in each metacell? Is there a Metacell function that answers that?

akhiadber commented 3 years ago

The mc@e_gc matrix is a genes by metacells matrix with the normalized fractions for each gene in each metacell. If you a looking for the UMI sum per gene per metacell, you can try something like: mc_sums = tgs_matrix_tapply(mat@mat[,names(mc@mc)], mc@mc, sum)

assuming you name your matrix and metacells objects "mat" and "mc"