genBart (version 1.0.1)

genFile: Generate and Update BART Result files

Description

Generate/Update BART file that can be directly uploaded into the BART app

Usage

genFile(meta, model.results = NULL, module.scores = NULL,
  dendrograms = NULL, qusage.results = NULL, roast.results = NULL,
  corr.results = NULL, project.name = "BART Project", folder.path = NULL)
updateFile(load.path = NULL, output.path = NULL, meta = NULL,
  model.results = NULL, module.scores = NULL, dendrograms = NULL,
  qusage.results = NULL, roast.results = NULL, corr.results = NULL,
  project.name = NULL)

Arguments

meta

A list of a single or multiple objects returned by metaData. Default is NULL.

model.results

A list of a single or multiple objects returned by genModelResults. Default is NULL.

module.scores

Object returned by genModScores. Default is NULL.

dendrograms

Object returned by clusterData. Default is NULL.

qusage.results

Object returned by runQgen. Default is NULL.

roast.results

Object returned by rBart. Default is NULL.

corr.results

A list of a single or multiple objects returned by crossCorr. Default is NULL.

project.name

String giving the name project name. Default is "BART Project".

folder.path

Path to create folder that BART file will be saved to. If NULL (default), BART folder will be created in the current working directory.

load.path

Folder path of BART file that needs to be updated.

output.path

Folder path to save updated BART file. If NULL (default), updated BART file will override the old one.

Details

genFile generates a formatted R data file (bartResults.rda) that can be uploaded into the BART web application. The file is created based on result objects returned by the various functions in genBart. Since BART can store and display results across multiple platforms at one time (e.g. RNA-seq, flow cytometry, metabolomics), some of the parameters (i.e. meta, model.results, corr.results) require the input objects to be wrapped in a list. The function saves the file in a folder whose name is given by project.name. The folder is created in the current working directory.

updateFile takes an existing BART file and allows the user to easily add and/or revise components. The user can override the old BART file by leaving output.path as NULL or give a new path in which to save the updated file.

Examples

# NOT RUN {
# Example data
data(tb.expr)
data(tb.design)

# Use first 100 probes to demonstrate
dat <- tb.expr[1:100,]

# Create desInfo object
meta.data <- metaData(y = dat, design = tb.design, data.type = "microarray", 
                    columnname = "columnname", long = TRUE, subject.id = "monkey_id",
                    baseline.var = "timepoint", baseline.val = 0, time.var = "timepoint", 
                    sample.id = "sample_id")
                    
# create BART file (minimal example)
genFile(meta = list(meta.data), folder.path = tempdir())                     

# generate module scores, normalize and cluster genes
mods <- genModScores(meta.data, modules)
data.norm <- normalizeData(meta = meta.data)
dendros <- clusterData(norm.data = data.norm)

# Update BART file with module scores and clustered genes
path <- paste0(tempdir(), "/", "BART Project")
updateFile(load.path = path, module.scores = mods, dendrograms = dendros)
# }