Description Usage Arguments Value
View source: R/write_pants_xl.R
Create directory; write CSV files with stats from feat.tab
for all features in each pathway, and the top
features that impact each pathway (even if they're outside the pathway); and write an Excel XLSX file using
writexl
that links to the CSVs.
1 | write_pants_xl(zscores, pwy.tab, feat.tab, Gmat, ker, name, ntop = 5)
|
zscores |
Matrix with rownames as feature names, and 1st column with z-scores to select high impact nodes.
Non- |
pwy.tab |
A table of pathway results. |
feat.tab |
Table of feature (e.g. gene) statistics and annotation, with |
Gmat |
Binary feature (e.g. gene) by pathway inclusion matrix, indicating which features are in which pathways. |
ker |
Laplacian kernel matrix representing the interaction network. |
name |
Name for the folder and Excel file that get written. Set to |
ntop |
Number of top features that most impact a pathway to include. |
Invisibly, a list with two components:
pwys.xl
Data frame representing written Excel file
pwy.csvs
List of data frames representing each written pathway CSV file
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