ballgown-constructor: constructor function for ballgown objects

Description

constructor function for ballgown objects

Usage

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

Arguments

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.

Value

an object of class ballgown

Details

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 file.path(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.

Examples

Run this code

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