zhengtaoxiao / single-cell-metabolic-landscape Goto Github PK

Hi zhengtaoxiao！
when i repeated your data, some errors produced.
error result as follows：

scimpute(file.path(outDir,"tumor.tpm"),infile="csv",outfile="csv",out_dir=file.path(outDir,"malignant_"),

• labeled=TRUE,labels=as.vector(labels_tumor),
• type="TPM",genelen=genelen,drop_thre=0.5,ncores=num_cores)
  [1] "reading in raw count matrix ..."
  [1] "number of genes in raw count matrix 23684"
  [1] "number of cells in raw count matrix 1167"
  Error in if (min(raw_count) < 0) { :
  missing value where TRUE/FALSE needed
  In addition: Warning message:
  In dir.create(out_dir, recursive = TRUE) :
  'dataset/NA/malignant_' already exists

Mine is only relatively shallow, so I do not know how to deal with, would like to ask you for advice. I hope you will give me your advice

Hello, I have a question about "TCGA_ pathway_activity". I don't know why this error occurred due to activity issues.
In code
TCGA_ exp_ file <- file.path("../Data/TCGA/",tumor,"exp.txt")
TCGA_ type_ file <- file.path("../Data/TCGA/",tumor,"type.txt")
I couldn't find these two files(exp.txt,type.txt) in the TCGA folder.
I sincerely look forward to your reply

Why did I get all these sce.rds, but not "selected_impute_sce.rds"?
thanks for your help.
Fan

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!

Hi Zhengtao,
Very nice work! I was wondering if your metabolic scoring algorithm can be used to compare the metabolic activity across different conditions for the same cell type (let's say, disease versus healthy)?
If so, what would you suggest me to do? I ran your pipeline in my dataset but no pathways are significant in disease versus healthy cells albeit there are significant changes of the metabolic genes between the two conditions. I tried to use another algorithm COMPASS but it took extremely long time to run so I still hope to use your approach if that's possible...
Many thanks in advance!