Description Usage Arguments Examples
This function calculates the correlation of gene expression with the inferred pseudo time.
1 2 | calc_correlation(full_gene_exprs, pseudo_time, type = "dcor",
order = F)
|
full_gene_exprs |
A gene (row) by cell (col) gene expression matrix with all genes. |
pseudo_time |
The pseudo development time / ordering of cells can be provided as input. Please leave order = F if pseudotime is provided |
type |
The type of correlation to calculate. "dcor" and "mic" are available (Distance correlation / Maximal Information Criterion). |
order |
Defaults to F. If pseudotime is provided, set to F. If an ordering of cells is provided, set to T. |
1 2 3 | dcor_result <- calc_correlation(full_exprs_matrix, redpath_pseudotime, type = "dcor")
mic_result <- calc_correlation(full_exprs_matrix, redpath_pseudotime, type = "mic")
selected_result <- gene_selection(full_exprs_matrix, redpath_pseudotime, dcor_result, mic_result, threshold = 0.5)
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