COMBIA (version 1.0.6)

readFluostarPlates: Read a file and process it to calculate the Survival indeces(S.I). This function calls other functions to complete its task. It reads a file to separate and regenerate the missing platekeys. Checks are performed to keep regenerated missing keyvalues in sync with data. It calculates survival indeces of the provided control wells, where wells should always be in triplet form that is control well range, empty well range and case well range. It can also handle the double plate experiments in which one plate is read twice and only one of them is selected in S.I calculations. Secondly it can also read the data from the file where a plate is read only one time, still it cope with variations if an experiment is repeated twice or many time in adjacent rows in the file.

Description

Read a file and process it to calculate the Survival indeces(S.I). This function calls other functions to complete its task. It reads a file to separate and regenerate the missing platekeys. Checks are performed to keep regenerated missing keyvalues in sync with data. It calculates survival indeces of the provided control wells, where wells should always be in triplet form that is control well range, empty well range and case well range. It can also handle the double plate experiments in which one plate is read twice and only one of them is selected in S.I calculations. Secondly it can also read the data from the file where a plate is read only one time, still it cope with variations if an experiment is repeated twice or many time in adjacent rows in the file.

Usage

readFluostarPlates(filename, separator = ",", noofrows_skip = 0,
  sheet = "1", readplates = 1, platetype, doubleplateexperiment = TRUE,
  keyposition, selectionkey, platekey, rowsperexperiment = 1, wells)

Arguments

filename

value of this argument should be path and filename.ext e=g "e:/optima.txt".

separator

is the sepration character within the file assigned to filename.

noofrows_skip

Number of the rows in the file that should be skipped before starting the data reading.

sheet

Need to use only when reading excel files. It is the number of the excel sheet to be read in a worksheet.

readplates

Number of the plates to read from a set of plates from an excel file, This feature is only workable with xls files.

platetype

Two types of plate formates are supported 384 and 96 wells.

doubleplateexperiment

This parameter can have TRUE & FALSE values only. It is set to TRUE when an experiment is read twice.

keyposition

It is the position of key in the header. Currently it is located at the second position but it can be at any position in the header.

selectionkey

value, that will be used during the selection of plate. Current value is 65000.

platekey

barcode of the plate whose wells you want to measure for Survival index

rowsperexperiment

It is the argument that specifies if the same experiment is repeated and how many times in a plate. If an experiment is repeated twice in adjacent rows then average of its values will be used in the SI calculation.

wells

This argument can take a list of arguments in the triplet form. Where first argument of triplet is the range of control wells, second argument is the range of empty wells while third one is the range of case wells. It is made so that in labs plates layouts can differ greatly. By using this triplet scheme one can handel a number of palte layouts. Values should be given in the according to plate range e-g a4:d5 means start from the a(1) row and first column and continue to d(4) row 5th column.

Value

Matrix of S.I.

Examples

# NOT RUN {
f <- system.file("extdata", "optima.log", package = "COMBIA")
platematrix <- readFluostarPlates(filename = f, platetype = "384", 
                                   keyposition=2, separator= "\t",     
                                   selectionkey = "65000", platekey = 7051,
wells = c( "c8:h8","c1:n1","c3:c7",    "c8:h8","c1:n1","c9:c11", 
           "c8:h8","c1:n1","e3:e7",     "c8:h8","c1:n1","e9:e11",
           "c8:h8","c1:n1","g3:g7",     "c8:h8","c1:n1","g9:g11" )
                                 )
# }