gate_flowClust_1d {openCyto} | R Documentation

## Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters.

### Description

We cluster the observations in `fr` into `K` clusters.

### Usage

    gate_flowClust_1d(fr, params, filterId = "", K = NULL, trans = 0,
      min.count = -1, max.count = -1, nstart = 1, prior = NULL,
      criterion = c("BIC", "ICL"), cutpoint_method = c("boundary",
      "min_density", "quantile", "posterior_mean", "prior_density"),
      neg_cluster = 1, cutpoint_min = NULL, cutpoint_max = NULL, min = NULL,
      max = NULL, quantile = 0.99, quantile_interval = c(0, 10),
      plot = FALSE, debug = FALSE, ...)

    flowClust.1d(fr, params, filterId = "", K = NULL, trans = 0,
      min.count = -1, max.count = -1, nstart = 1, prior = NULL,
      criterion = c("BIC", "ICL"), cutpoint_method = c("boundary",
      "min_density", "quantile", "posterior_mean", "prior_density"),
      neg_cluster = 1, cutpoint_min = NULL, cutpoint_max = NULL, min = NULL,
      max = NULL, quantile = 0.99, quantile_interval = c(0, 10),
      plot = FALSE, debug = FALSE, ...)

### Arguments

`fr` | a `flowFrame` object
`params` | `character` channel to be gated on
`filterId` | A `character` string that identifies the filter created.
`K` | the number of clusters to find
`trans, min.count, max.count, nstart` | some flowClust parameters. see `flowClust`
`prior` | list of prior parameters for the Bayesian `flowClust`. If `NULL`, no prior is used.
`criterion` | a character string stating the criterion used to choose the best model. May take either "BIC" or "ICL". This argument is only relevant when `K` is `NULL` or if `length(K) > 1`. The value selected is passed to `flowClust`.
`cutpoint_method` | How should the cutpoint be chosen from the fitted `flowClust` model? See Details.
`neg_cluster` | integer. The index of the negative cluster. The cutpoint is computed between clusters `neg_cluster` and `neg_cluster + 1`.
`cutpoint_min` | numeric value that sets a minimum thresold for the cutpoint. If a value is provided, any cutpoint below this value will be set to the given minimum value. If `NULL` (default), there is no minimum cutpoint value.
`cutpoint_max` | numeric value that sets a maximum thresold for the cutpoint. If a value is provided, any cutpoint above this value will be set to the given maximum value. If `NULL` (default), there is no maximum cutpoint value.
`min` | a numeric value that sets the lower bound for data filtering. If `NULL` (default), no truncation is applied.
`max` | a numeric value that sets the upper bound for data filtering. If `NULL` (default), no truncation is applied.
`quantile` | the quantile for which we will find the cutpoint using the quantile `cutpoint_method`. If the `cutpoint_method` is not set to `quantile`, this argument is ignored.
`quantile_interval` | a vector of length 2 containing the end-points of the interval of values to find the quantile cutpoint. If the `cutpoint_method` is not set to `quantile`, this argument is ignored.
`plot` | logical value indicating that the fitted `flowClust` model should be plotted along with the cutpoint
`debug` | `logical` indicating whether to carry the prior and posterious with the gate for debugging purpose. Default is FALSE.
`...` | additional arguments that are passed to `flowClust`

### Details

By default, the cutpoint is chosen to be the boundary of the first two clusters. That is, between the first two cluster centroids, we find the midpoint between the largest observation from the first cluster and the smallest observations from the second cluster. Alternatively, if the `cutpoint_method` is `min_density`, then the cutpoint is the point at which the density between the first and second smallest cluster centroids is minimum.

### Value

a `rectangleGate` object consisting of all values beyond the cutpoint calculated

### Examples

    ## Not run:
     gate <- gate_flowClust_1d(fr, params = "APC-A", K =2) # fr is a flowFrame

    ## End(Not run)

[Package openCyto version 1.20.2 Index]