SOUNDManager-class: Managing SOUNDBoard Reports

In Bioconductor/SOUNDBoard: Statistically-informed Multi-Omics Reports for Tumor and Other Boards

Description

This page describes facilities for managing SOUNDBoard reports. Management tasks include (1) creating template reports; (2) publishing as temporary documents during development; and (3) publishing as final reports for communciation with board members.

Usage

SOUNDManager(board_directory, sql_template_path, rmd_template_path,
  user = "soundboard", host = "localhost",
  deploy_path = file.path("~/srv", basename(board_directory)),
  port = "3838", path = "")

deploy_path(object)

urls(object)

deploy(x, dryrun = TRUE, options = "-avz")

## S4 method for signature 'SOUNDManager'
show(object)

Arguments

board_directory	character(1) Local directory where board, case, and assay elements are marshalled.
sql_template_path	character(1) path to existing SQL template file, containing table and templated query definitions. The default is system.file(package="SOUNDBoard", "template", "SOUNDBoard.sql") (also use this file to model your own templates).
rmd_template_path	character(1) (optional) path to existing Rmd template file, containing an R-markdown file to be displayed to SOUNDBoard members. If no Rmd files exist in board_directory and rmd_template_path is missing, system.file(pacakge="SOUNDBoard", "template", "SOUNDBoard.Rmd") is copied to board_directory. If a file with basename(rmd_template_path) already exists in board_directory, a warning is issued and the existing file not replaced.
user	character(1) name of SOUNDBoard user from which applications are deployed. Default: "soundboard"
host	character(1) URI of deployment server directory.
deploy_path	character(1) server path to directory where SOUNDBoard reports are deployed to.
port	character(1) communation endpoint from the host.
path	character(1) http: path to SOUNDBoard reports.
object	SOUNDManager-class instance.
dryrun	logical(1) rsync to deploy_path()?
options	character(1) rsync options.

Bioconductor/SOUNDBoard documentation built on May 6, 2019, 7:52 a.m.