Accessor and Dependency Package Errors

[mattobny]

Continuing @Umaarasu discussion thread as it is more fitting for this to be placed here.

[mattobny]

@Umaarasu

To address one part of the previous thread, the code below uses an internal accessor, get_expression_values:

rank_matrix = makeSignMatrixRank(sc_matrix = get_expression_values(giotto_SC, 
values = "normalized",output = "matrix"), sc_cluster_ids = pDataDT(giotto_SC)$Class)

We apologize that this caused an error. The correct code, utilizing the proper accessor getExpression, is below:

sc_expression_norm = getExpression(giotto_SC,
                                  values = "normalized",
                                  output = "matrix")

rank_matrix = makeSignMatrixRank(sc_matrix = sc_expression_norm,
                                sc_cluster_ids = pDataDT(giotto_SC)$Class)

I understand that code using some internal accessor(s) lives on the website. I am actively updating the site to address this.

[Umaarasu]

Thanks @mattobny . This helps with the error. While the code works fine for the example data you provided, how would it be for publicly downloaded ones. For example I am trying to use data from mouse atlas paper. How would you upload the data from there? They give it as .Robj

[mattobny]

Glad to hear.

Based on the previous commentary, I assume you seek to make a sign matrix for rank enrichment. In that case, you would need to extract the RNA expression data from this .Robj along with the corresponding cell IDs. Then you can provide these as arguments in matrix format to sc_matrix and sc_cluster_ids, respectively, in makeSignMatrixRank()