Confusing details in create_profile_matrix documentation

[oospina]

Hello! While reading the documentation for the create_profile_matrix function, I notice it asks for a cell x gene matrix (which I understand as cells in rows). However, when looking at the tutorial ("Use of SpatialDecon in a large GeoMx dataset with GeomxTools") it looks like it uses a gene x cell matrix (genes in rows). I went and transposed my data and passed that as input, since it looks like your function makes an attempt to check that genes and cells are in the correct position in this part:

if(!any(names(cellTypes) %in% colnames(mtx)) & 
   any(names(cellTypes) %in% rownames(mtx))){
      print("Transposing Matrix")
      mtx<- t(mtx)
}

But the function crashes in that part:

[1] "Transposing Matrix"
Error in t.default(mtx) : argument is not a matrix

Is it possible that what the function actually uses is a gene x cell matrix (genes in rows) as opposed to what the documentation says?

Thank you!

Oscar

[maddygriz]

Hi Oscar,

It is indeed a gene x cell (genes in rows) matrix that is expected. I will update the documentation.

Thanks, Maddy

[oospina]

Thanks for the clarification!