loadAll: Data importing

In OperaMate: An R package of Data Importing, Processing and Analysis for Opera High Content Screening System

Description

Initializes a list of expData objects from the Columbus system reports.

Usage

loadAll(cellformat = NULL, datapath = "./",
  egFilename = getOption("opm.filename.example"), well.digits = 2,
  platemap = NULL)

Arguments

cellformat	character specifying the format of the reports. Enable when platemap is NULL.
datapath	character specifying the location of the reports. Enable when platemap is NULL.
egFilename	a file name example
well.digits	the digits of the well column in the well-gene
platemap	data frame. See an example as platemap.

Details

To facility the automatic file name parsing, the reports obtained from Columbus system should be of the same format, and located under the same directory. Users can obtain this plate specification table for further modification. An example of the table can be referred by platemap. After modification, users can submit a plate speficication data frame to parameter platemap. The data format supported for the reports are "Tab" and "Matrix". If the reports are of other cellformats, you can specify its cellformat and rewrite the function parseTemplete to import the data seperately.

An example of egFilename = list(eg.filename = "0205-s2-01.txt", rep.id = "s2", exp.id = "01", sep = "-", barcode = "DSIMGA01"). well.digits: In the well-gene specification file, if the well ID is B1, B2, ..., B11, the well.digit = 1; while B01, B02, ..., B11, the well.digit = 2; and B001, B002, ..., B011, the well.digit =3.

Value

a list of expData objects

Examples

# Data frame \code{platemap} provided
data(platemap)
platemap$Path <- file.path(
system.file("Test", package = "OperaMate"), platemap$Path)
lstPlates <- loadAll(platemap = platemap)
#
# Consistent file name format
datapath <- file.path(system.file("Test", package = "OperaMate"), "Tab")
egFilename <- list(eg.filename = "Tab.130504-s1-01.txt",
rep.id = "s1", exp.id = "01", sep = "-",
barcode = "DSIMGA01")
lstPlates <- loadAll(cellformat = "Tab", datapath = datapath,
egFilename = egFilename, well.digits = 2)
#
lstPlates[[1]]

OperaMate documentation built on Nov. 17, 2017, 1:55 p.m.