fg_feat_edge_specenr: Generates the SpecEnr edge feature.

In aya49/flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequency

Generates the SpecEnr edge feature.

Description

Generates the SpecEnr edge feature and returns it inside the flowGraph object.

Usage

fg_feat_edge_specenr(fg, no_cores = 1, overwrite = FALSE)

Arguments

fg	flowGraph object.
no_cores	An integer indicating how many cores to parallelize on.
overwrite	A logical variable indicating whether to overwrite the existing proportion edge feature if it exists.

Details

Given a flowGraph object, fg_feat_edge_SpecEnr returns the same flowGraph object with an additional SpecEnr and expected proportions expect_prop edge feature and its meta data. The expected proportions edge feature is calculated by taking the ratio of the child nodes' (e.g. A+B+) expected proportion value over its parent nodes' (e.g. A+) actual proportion value. The SpecEnr feature is the actual over expected proportion ratio, logged. The edge feature matrix has column names <from>_<to> e.g. A+_A+B+.

Value

flowGraph object containing the proportion edge feature.

See Also

flowGraph-class fg_feat_node_prop fg_feat_node_specenr 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)

 fg <- fg_feat_edge_specenr(fg)

aya49/flowGraph documentation built on Feb. 4, 2024, 6:40 p.m.