ballgown-constructor: constructor function for ballgown objects
In alyssafrazee/ballgown: Flexible, isoform-level differential expression analysis

Description Usage Arguments Details Value Author(s) See Also Examples

constructor function for ballgown objects

ballgown(
  samples = NULL,
  dataDir = NULL,
  samplePattern = NULL,
  bamfiles = NULL,
  pData = NULL,
  verbose = TRUE,
  meas = "all"
)

`samples`	vector of file paths to folders containing sample-specific ballgown data (generated by `tablemaker`). If `samples` is provided, `dataDir` and `samplePattern` are not used.
`dataDir`	file path to top-level directory containing sample-specific folders with ballgown data in them. Only used if `samples` is NULL.
`samplePattern`	regular expression identifying the subdirectories of\ `dataDir` containing data to be loaded into the ballgown object (and only those subdirectories). Only used if `samples` is NULL.
`bamfiles`	optional vector of file paths to read alignment files for each sample. If provided, make sure to sort properly (e.g., in the same order as `samples`). Default NULL.
`pData`	optional `data.frame` with rows corresponding to samples and columns corresponding to phenotypic variables.
`verbose`	if `TRUE`, print status messages and timing information as the object is constructed.
`meas`	character vector containing either "all" or one or more of: "rcount", "ucount", "mrcount", "cov", "cov_sd", "mcov", "mcov_sd", or "FPKM". The resulting ballgown object will only contain the specified expression measurements, for the appropriate features. See vignette for which expression measurements are available for which features. "all" creates the full object.

Because experimental data is recorded so variably, it is the user's responsibility to format pData correctly. In particular, it's really important that the rows of pData (corresponding to samples) are ordered the same way as samples or the dataDir/samplePattern combo. You can run list.files(path = dataDir, pattern = samplePattern) to see the sample order if samples was not used.

If you are creating a ballgown object for a large experiment, this function may run slowly and use a large amount of RAM. We recommend running this constructor as a batch job and saving the resulting ballgown object as an rda file. The rda file usually has reasonable size on disk, and the object in it shouldn't take up too much RAM when loaded, so the time and memory use in creating the object is a one-time cost.

an object of class ballgown

Leonardo Collado-Torres, Alyssa Frazee

ballgownrsem, for loading RSEM output into a ballgown object

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bg = ballgown(dataDir=system.file('extdata', package='ballgown'),
    samplePattern='sample')
pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=10))