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# runDM

Source: `R/dim_reduction.R`
`runDM.Rd`

Run Diffusion Map dimensionality reduction.

## Usage

    runDM(
      fcd,
      input_type,
      data_slot,
      k = 10,
      seed = 91,
      prefix = NULL,
      nPC = ncol(fcd[[input_type]][[data_slot]]),
      markers = colnames(fcd$expr[[data_slot]]),
      discard = FALSE
    )

## Arguments

fcd

  flow cytometry dataset.

input_type

  data to use for the calculation, e.g. "expr" or "pca".

data_slot

  data slot to use for the calculation, e.g. "orig" or "norm".

k

  K used for the analysis. Default = 10.

seed

  A seed is set for reproducibility.

prefix

  Optional prefix for the slot name of the output.

nPC

  Number of principal components to use for the analysis. Default = All.

markers

  Vector of marker names to include or exclude from DM calculation according to the discard parameter. See functions `used_markers` and `measured_markers` for the extraction of markers directly from the condor object.

discard

  LOGICAL if the markers specified should be included, "False", or excluded, "True", from the DM calculation. Default = F.

## Value

The function returns a fcd including a data frame with the DM coordinates saved in `fcd$diffmap`. The name of the output consists of the prefix (if given) and the data slot. If a `nPC` is given it will be added to the output name.

## Details

runDM

See [Philipp Angerer et al. (2015): destiny: diffusion maps for large-scale single-cell data in R. Helmholtz-Zentrum München.] (http://bioinformatics.oxfordjournals.org/content/32/8/1241)