fg_feat_node_specenr {flowGraph} | R Documentation

## Generates the SpecEnr node feature.

### Description

Generates the SpecEnr node feature and returns it inside the returned flowGraph object.

### Usage

    fg_feat_node_specenr(fg, no_cores = 1, feature = "prop", overwrite = FALSE)

### Arguments

`fg` | flowGraph object
`no_cores` | An integer indicating how many cores to parallelize on.
`feature` | A string indicating feature name; this is the feature SpecEnr will be calculated on.
`overwrite` | A logical variable indicating whether to overwrite the existing SpecEnr node feature if it exists.

### Details

Given a flowGraph object, `fg_feat_node_specenr` returns the same flowGraph object with an additional `SpecEnr` and `expect_prop` `node` feature and its meta data. The expected proportions feature is made using the `prop` `node` and `edge` features; therefore, the returned flowGraph will also contain these two features. For details on how these feature is calculated.

### Value

flowGraph object containing the SpecEnr node feature.

### References

Yue A, Chauve C, Libbrecht M, Brinkman R (2019). “Identifying differential cell populations in flow cytometry data accounting for marker frequency.” BioRxiv, 837765.

### See Also

`flowGraph-class` `fg_feat_node_prop` `fg_add_feature` `fg_get_feature` `fg_rm_feature` `fg_get_feature_desc`

### Examples

     no_cores <- 1
     data(fg_data_pos30)
     fg <- flowGraph(fg_data_pos30$count, class=fg_data_pos30$meta$class,
                     prop=FALSE, specenr=FALSE,
                     no_cores=no_cores)

     # SpecEnr is by default calculated based on proportions
     fg <- fg_feat_node_specenr(fg, no_cores=no_cores)

     # SpecEnr can be calculated for other feature values too
     fg <- fg_feat_node_specenr(fg, feature="count")

     show(fg)

[Package flowGraph version 1.2.0 Index]