standardize-GatingSet: The tools to standardize the tree structures and channel...

In RGLab/flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

The tools to standardize the tree structures and channel names.

Description

gs_split_by_tree(x)

gs_split_by_channels(x)

gs_check_redundant_nodes(x)

gs_remove_redundant_nodes(x, toRemove)

gs_remove_redundant_channels(gs)

gs_update_channels(gs, map, all = TRUE)

gh_pop_move(gh, node, to)

gs_pop_set_visibility(x, y, FALSE)

Details

In order to merge multiple GatingSets into single GatingSetList, the gating trees and channel names must be consistent. These functions help removing the discrepancies and standardize the GatingSets so that they are mergable.

gs_split_by_tree splits the GatingSets into groups based on the gating tree structures.

gs_split_by_channels split GatingSets into groups based on their flow channels.

gs_check_redundant_nodes returns the terminal(or leaf) nodes that makes the gating trees to be different among GatingSets and thus can be considered to remove as redundant nodes.

gs_remove_redundant_nodes removes the terminal(or leaf) nodes that are detected as redundant by gs_check_redundant_nodes.

gs_remove_redundant_channels remove the redundant channels that are not used by any gate defined in the GatingSet.

gs_update_channels modifies the channel names in place. (Usually used to standardize the channels among GatingSets due to the letter case discrepancies or typo).

gh_pop_move inserts a dummy gate to the GatingSet. Is is useful trick to deal with the extra non-leaf node in some GatingSets that can not be simply removed by gs_remove_redundant_nodes

gs_pop_set_visibility hide a node/gate in a GatingSet. It is useful to deal with the non-leaf node that causes the tree structure discrepancy.

RGLab/flowWorkspace documentation built on March 17, 2024, 2:24 p.m.