dataCollective-class: Class Definition for Storing jonesDatum objects with methods...

In Khlick/jonesDataClass: Class Objects To Manage Calcium Imaging Data From Dr. Jones

Description

Class Definition for Storing jonesDatum objects with methods to access data, subest traces, append/remove files,

Fields

files

Char vector containing full paths to data files (.xlsx)

names

no Input. Contains names of files loaded

data

no Input. Contains named list of jonesDatum objects

nFiles

noInput. Contains the count of currently loaded

Methods

extractArea(dataNames)

Extracts data.frames of Area from supplied dataNames. Always returns named list.

extractData(dataNames, type = c("adjusted", "standardized", "raw", "background", "corrected"), asList = FALSE)

Extracts matrix of data from supplied dataNames. Always returns named list.
Argument, asList, set to TRUE will extract each dataFile's data as a list of lists rather than as a dataList object (default).

extractDatum(dataName, copy = FALSE)

Gets the jonesDatum object for a single dataName.
Use copy = FALSE for chaining (default). Set to TRUE if a copy is desired, otherwise changes to the output object will affect the original. In other words, setting to TRUE will mimic R's copy-on-modify behavior.

extractIDs(dataNames)

Extracts data.frames of Area from supplied dataNames. Always returns named list.

extractROI(dataNames)

Extracts data.frames of ROIs from supplied dataNames. Always returns named list.

getDetails(type = "confluence", asUnique = FALSE, ...)

Returns possible inputs for type. If asUnique=TRUE or data values as vector.
Possible inputs for type are:

• SampleRate: Recording rate in frames per second.

• TreatmentStart: Time of Treatment, if applicable.

• nCells: Number of cells in the dataset.

• HasBackground: Whether or not a background correction performed.

• ExperimentDate: Date of the original collection.

• CellType: What kind of cells are we dealing with.

• PassageNumber: The passage number given as P#.

• MediaSupl: What other factors were introduced into the media.

• StarvedLength: How long were the cells serum starved prior to collection.

• confluence: How conlfuent, 0-100 percent, were the cells at collection time.

• checkConfluence: Provide prcnt [0,100] in the ... arg. Returns boolean.

• primaryTreatment: Get the primary treatment, either NA or ET1

• secondaryTreatment: Get teh secondary treatmetn, either NA or IL1b

• endothelin: Returns TRUE if ET1 was applied.

• interleukin: Returns TRUE if IL1b was applied.

getMatches(confluence = NULL, endothelin = NULL, interleukin = NULL)

getMatches returns a vector of data file names matching provided criteria. Values left at default will not be checked, thus an empty call will get all names. Acceptable values for input arguments are:

• confluence Must be NULL or NUMERIC on [0,100]. Checking for percent confluence.

• endothelin Must be NULL or BOOLEAN. Checks for ET1 treatment only.

• interleukin Must be NULL or BOOLEAN. Checks for IL-1b treatment only.

pop(first = FALSE)

Removes and returns last datum unless arg first = TRUE.

push(newFiles, ...)

Appends newfiles that do not already exist

save(pathName, objectName = "", ...)

Save the current object on the file in R external object format.

size()

Get the size of the object in memory.

subset(dataNames, inplace = FALSE)

Returns a copy, unless inplace=TRUE then data are dropped.

Khlick/jonesDataClass documentation built on May 26, 2019, 4:37 p.m.