loadAll: Data importing

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.

Value

a list of expData objects

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.

Examples

Run this code

# 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]]