keyword-mutators: Methods to alter keywords in 'cytoframe', 'cytoset',...

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

Description

These methods allow for direct insertion, deletion, or renaming of keywords in cytoframe, cytoset, GatingHierarchy, or GatingSet objects.

Usage

cf_keyword_insert(cf, keys, values)

cf_keyword_delete(cf, keys)

cf_keyword_rename(cf, old_keys, new_keys)

cf_keyword_set(cf, keys, values)

cs_keyword_insert(cs, keys, values)

cs_keyword_delete(cs, keys)

cs_keyword_rename(cs, old_keys, new_keys)

cs_keyword_set(cs, keys, values)

gh_keyword_insert(gh, keys, values)

gh_keyword_delete(gh, keys)

gh_keyword_rename(gh, old_keys, new_keys)

gh_keyword_set(gh, keys, values)

gs_keyword_insert(gs, keys, values)

gs_keyword_delete(gs, keys)

gs_keyword_rename(gs, old_keys, new_keys)

gs_keyword_set(gs, keys, values)

Arguments

cf	a cytoframe
keys	the keyword names to insert/delete/replace – single value or vector
values	the values to associate with the supplied keywords – single value or vector of sample length as keys
old_keys	the old keyword name (for renaming)
new_keys	the new keyword name (for renaming)
gh	a GatingHierarchy
gs	a GatingSet

Details

Each of the methods taking two character vectors (keys/values or old_keys/new_keys) will also accept a single named vector for flexibility in usage.

For the functions that take a vector of keys and a vector of values (the keyword_insert and keyword_set functions), the names of this vector should be the keys to which the values of the vector will be assigned.

For the keyword_rename functions, the names of this vector should be the existing keyword names (old_keys) while the values should be the replacement keyword names (new_keys).

See examples for details

Examples

library(flowCore)
data(GvHD)
cs <- flowSet_to_cytoset(GvHD[1:2])

keys <- c("CYTNUM", "CREATOR")

# Values before changes
keyword(cs, keys)

# Set two keyword values using separate key and values vectors
values <- c("E3598", "CELLQuest  3.4")
cs_keyword_set(cs, keys, values)

# Values after changes
keyword(cs, keys)

# Change the values again using a single named vector
values <- c("E3599", "CELLQuest  3.5")
names(values) <- keys
cs_keyword_set(cs, values)

# Values after changes
keyword(cs, keys)

flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.