write_pants_xl: Write Excel XLSX file with links to CSVs

Description Usage Arguments Value

View source: R/write_pants_xl.R

Description

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.

Usage

1
write_pants_xl(zscores, pwy.tab, feat.tab, Gmat, ker, name, ntop = 5)

Arguments

zscores

Matrix with rownames as feature names, and 1st column with z-scores to select high impact nodes. Non-NA values should be finite.

pwy.tab

A table of pathway results.

feat.tab

Table of feature (e.g. gene) statistics and annotation, with score column.

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 NA to avoid writing output.

ntop

Number of top features that most impact a pathway to include.

Value

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


jdreyf/PANTS documentation built on July 18, 2019, 10:12 a.m.