readDBFData: Function for reading dbf files into R in accordance with...

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

View source: R/dataflow.R

Description

This function is used read dBase files into R according to a specified protocol.

Usage

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readDBFData(A.data, update = TRUE, perl= "perl", well.id = "WELLNUM", 
            absorbance.id  = "M1", 
            discard.lines  = c(1, 2), dosevar = "Concentration",
            additivevar = "Additive", controlval = "Control",
            backgroundval = "Background", mistakeval = "X", 
            remove.rows = c("A","H"), remove.cols = c(1, 12), 
            progressbar = "text", verbose= FALSE, save = TRUE, 
            shiny.input = NULL, session = NULL)

Arguments

A.data

An A.data object created by the function createMetaData.

update

Should the analysis be updated or run from scratch. Defaults to TRUE.

perl

The path to the perl.exe.

well.id

Name of the coloumn in the .dbf file containg well id's. Defeaults to "WELLNUM".

absorbance.id

Name of the coloumn in the .dbf file containg absorbance values. Defeaults to "M1".

discard.lines

A vector of linenumber that are to be discarded from the .dbf fiel. Defeaults to c(1, 2)

dosevar

Name of the column that contains concentration values in protocol.

additivevar

Name of the column that contains information regarding what each well values in protocol.

controlval

Value indicating that the cell line is untreated for the column defined in additivevar. Defeaults to Control

backgroundval

Value indicating that the well is used to measure background for the column defined in additivevar. Defeaults to Background

mistakeval

Value indicating that the particular well should not be used for analysis. This is specified in the setup part of the protocol where the default value X denote a mistake.

remove.rows

Vector of row indices that should be discarded according to the plate. Defeaults to c("A", "H") indicating that the border wells should be removed for a 96 well plate.

remove.cols

Vector of column indices that should be discarded according to the plate. Defeaults to c("1", "12") indicating that the border wells should be removed for a 96 well plate.

progressbar

The type of progress bar used to show how far along the function is. Can be either "window", text or none.

verbose

Should the function indicate what experiment it is currently reading. Defaults to FALSE.

save

Should the data be saved. Defeaults to TRUE.

shiny.input

Used for the shiny server.

session

Used for the shiny server.

Details

This function is used for reading the protocols defining the setup for each plate and the associated dbf files storing the absorbance measures into R. Because of the nature of the function no examples of function usage is presented here. Instead you should look at the Sweave document accompanying the R package.

Value

The ouput of the function is an A.data object of class Absorbance. This is a list with the following component

meta.list

This is a list of meta data objects.

call

A list containing information regarding the call to the function.

auxiliary

List of auxiliary data used by other functions.

data

List of data frames. The Absorbance data are stored in raw.data and the protocols are stored in protocols

Note

After the data have been read into R the need to be preprocessed. If any drug colour correction plates have been established continue to the funktion drugColorCorrection otherwise continue to the function bgModel.

Author(s)

The function was written at department of haematology, Aalborg University Hospital and maintained by Steffen Falgreen.

References

Steffen Falgreen et al. Exposure time independent summary statistics for assessment of drug dependent cell line growth inhibition (2013)

See Also

drugColorCorrection, bgModel

Examples

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##  Since this function is for reading data into R there are no examples of the usage
## See the associated Sweave document for detailed usage.

HaemAalborg/DoseR documentation built on Jan. 17, 2021, 7:40 a.m.