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# Helper function within cyCONDOR

Source: `R/misc.R`
`checkInput.Rd`

`checkInput()` is a helper function within several cyCONDOR functions for visualization and differential testing. It checks availability if selected 1st level elements (clustering) and 2nd level elements (expr_slot, cluster_slot, cell_anno), and 3rd level variable names in cluster_slot and cell_anno are present. In order to ensure proper functioning, all arguments that are strictly necessary in the parent function and for which no default can be given, should NOT be set to NULL. Please note that this function does not give an error, when group_var, sample_var or pair_var were set to NULL by user in parent function, since these arguments are sometimes optional in the functions.

## Usage

    checkInput(
      fcd,
      check_expr_slot = F,
      check_cluster_slot = F,
      check_cell_anno = F,
      check_reduction = F,
      expr_slot = NULL,
      cluster_slot = NULL,
      cluster_var = NULL,
      reduction_method = NULL,
      reduction_slot = NULL,
      group_var = NULL,
      sample_var = NULL,
      pair_var = NULL
    )

## Arguments

fcd

  flow cytometry dataset

check_expr_slot

  logical indicating if expr_slot should be checked

check_cluster_slot

  logical indicating if cluster_slot should be checked

check_cell_anno

  logical indicating if cell_anno should be checked

check_reduction

  logical indicating if reduction_method should be checked

expr_slot

  set to NULL (default) if expr_slot is not needed in parent function, set equal to expr_slot if expr_slot string should be checked

cluster_slot

  set to NULL (default) if cluster_slot is not needed in parent function, set equal to cluster_slot if cluster_slot string should be checked

cluster_var

  set to NULL (default) if cluster_var is not needed in parent function, set equal to cluster_var if cluster_var string should be checked

reduction_method

  set to NULL (default) if reduction_method is not needed in parent function, set equal to reduction_method if reduction_method string should be checked

reduction_slot

  set to NULL (default) if reduction_slot is not needed in parent function, set equal to reduction_slot if reduction_slot string should be checked

group_var

  set to NULL (default) if group_var is not needed in parent function, set equal to group_var if group_var string should be checked

sample_var

  set to NULL (default) if sample_var is not needed in parent function, set equal to sample_var if sample_var string should be checked

pair_var

  set to NULL (default) if pair_var is not needed in parent function, set equal to pair_var if pair_var string should be checked

## Value

`checkInput()` returns an stop message if one of the checks fails.

## Details

checkInput