genFile: Generate and Update BART Result files
In jcardenas14/genBART: Generate 'BART' File

Description Usage Arguments Details Examples

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

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)

`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.

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.

# 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)