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zhengtaoxiao / Single-Cell-Metabolic-Landscape

Pipeline for characterizing metebolic heterogeneity from single-cell RNA-seq data
MIT License
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about "#some genes occur in multiple pathways" #4

Open zhangman20 opened 4 years ago

zhangman20 commented 4 years ago

in 5-PathwayActivity/scRNA_pathway_activity.R, when I run this:

some genes occur in multiple pathways.

gene_pathway_number <- num_of_pathways(pathway_file,rownames(selected_impute_sce [rowData(selected_impute_sce)$metabolic]) error occured: Error in num_of_pathways(pathway_file, rownames(selected_impute_sce)[rowData(selected_impute_sce)$metabolic]) : could not find function "num_of_pathways"

How to solve this problem? Thanks!

zhengtaoxiao commented 3 years ago

This function is defined in "utils.R", you can load it by using source("utils.R")

WANNQI commented 1 year ago

in 5-PathwayActivity/scRNA_pathway_activity.R, when I run this: #some genes occur in multiple pathways. gene_pathway_number <- num_of_pathways(pathway_file,rownames(selected_impute_sce [rowData(selected_impute_sce)$metabolic]) error occured: Error in num_of_pathways(pathway_file, rownames(selected_impute_sce)[rowData(selected_impute_sce)$metabolic]) : could not find function "num_of_pathways"

How to solve this problem? Thanks!

Do you met some errors in the step 2_imputation ? how do you deal with them ? I mets some errors, but there is no answers in the column of Issues. Can you help me? Thanks very much.