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modify assay with additional data

Source: R/manage_additional_metadata.R
modifyData.Rd

Reduce dimensionality of an assay by dropping extra data or combining variables.

Usage

modifyData(x, ...)

# S3 method for drug_name2
modifyData(x, option, keep, ...)

# S3 method for data_source
modifyData(x, option, keep, ...)

# S3 method for default
modifyData(x, option, keep, ...)

Arguments

x

a data.table containing an assay

...

additional arguments passed to methods

option

character string specifying the action to be taken, see Details

keep

character string specifying the value of the active variable that will be kept

Value

modified object

Details

If an essay extracted from a SummarizedExperiment contains additional information, i.e. factors beyond DrugName and CellLineName, that information will be treated in one of three ways, depending on the value of option:

  • drop: Some information will be discarded and only one value of the additional variable (chosen by the user) will be kept.

  • toDrug: The information is pasted together with the primary drug name. All observations are kept.

  • toCellLine: As above, but pasting is done with cell line name.

Depending on the type of additional information, the exact details will differ. This is handled in the app by adding special classes to the data tables and dispatching to S3 methods.

Following modification, the additional columns are discarded.

Methods (by class)

  • modifyData(drug_name2): includes the name and concentration of the second drug

  • modifyData(data_source): includes the data source

  • modifyData(default): includes the name of other additional variables

Examples

dt <- data.table::data.table(a = as.character(1:10), b = "data")
dt <- addClass(dt, "a")
modifyData(dt, "average", keep = "b")
#>         b
#>    <char>
#> 1:   data