S3 ParseInput function

Internal Function. Convert the input data to FlowSOM object ready to be processed. Many of the parameters are used by FlowSOM's ReadInput function. The description for these parameters are taken from FlowSOM.

Usage

ParseInput(
  inputFiles,
  compensate,
  spillover,
  transform,
  toTransform,
  transformFunction,
  scale,
  scaled.center,
  scaled.scale,
  silent,
  colsToUse,
  ...
)

# S3 method for class 'character'
ParseInput(
  inputFiles,
  compensate,
  spillover,
  transform,
  toTransform,
  transformFunction,
  scale,
  scaled.center,
  scaled.scale,
  silent,
  colsToUse,
  ...
)

# S3 method for class 'list'
ParseInput(
  inputFiles,
  compensate,
  spillover,
  transform,
  toTransform,
  transformFunction,
  scale,
  scaled.center,
  scaled.scale,
  silent,
  colsToUse,
  ...
)

# S3 method for class 'data.table'
ParseInput(
  inputFiles,
  compensate,
  spillover,
  transform,
  toTransform,
  transformFunction,
  scale,
  scaled.center,
  scaled.scale,
  silent,
  colsToUse,
  timepointCol,
  timepoints
)

Arguments

inputFiles

The list containing the input data

compensate

Whether to run data compensation

spillover

The spillover matrix to compensate

transform

Whether to run data transformation

toTransform

column names or indices to transform

transformFunction

The transform function to run

scale

Whether to scale the data

silent

Whether to show progress updates

...

Additional arguments used if inputFiles is a data.table object

timepointCol

A character denoting the column in data.frame that corresponds to the time-point each cell belongs to

timepoints

A vector of time-points.

scale.center

See base::scale

scale.scale

See base::scale

colToUse

Which column to be used by TrackSOM

Value

FlowSOM object

Methods (by class)

• ParseInput(character): Process vector of characters input

• ParseInput(list): Process list of data.frames input

• ParseInput(data.table): Process data.table input