cqc_match_update: Manual update/delete the match report

View source: R/cqc_match.R

cqc_match_updateR Documentation

Manual update/delete the match report


There are cases that the automatic string match from ‘cqc_match' can’t resolve. This function provides the remedy to manually update the match result.


cqc_match_update(x, map, group_id = NULL)

cqc_match_delete_unmatched(x, map, group_id = NULL)

cqc_match_remove(x, map, group_id = NULL)



'cqc_match_result_and_solution' object generated by "cqc_match"


For cqc_match_update, it is a named vector that provides the paired strings(i.e. old value vs new value). For cqc_match_remove or cqc_match_delete_unmatched, it is a character vector that provides the items to be removed from matched pairs or mark the unmatched items for deletion.


the group to update. If NULL, then operate on all groups


cqc_match_update() matches the items from target groups to the reference by the named vector through 'map' argument. cqc_match_remove() undo the matching that are produced either from cqc_match_update or cqc_match() cqc_match_delete_unmatched() forces the unmatched items marked for deletion.


fcs_files <- list.files(system.file("extdata", "GvHD_QC", package = "cytoqc"), full.names = TRUE)
qc_cf_list <- cqc_load_fcs(fcs_files)
groups <- cqc_check(qc_cf_list, type = "marker")
match_result <- cqc_match(groups, ref = 3)

# add the matching pairs to the auto-matching results
match_result <- cqc_match_update(match_result, map = c("PTPRC PE" = "CD45 PE"), group_id = 5)

# You can delete any match added manually or automatically by cqc_match
match_result <- cqc_match_remove(match_result, "PTPRC PE", group_id = 5)

# or mark selected items for deletion
#match_result <- cqc_drop_unmatched(match_result, "PTPRC PE", group_id = 5)

# You can also omit the group_id to apply to all groups
match_result <- cqc_match_update(match_result, map = c("PTPRC PE" = "CD45 PE"))

RGLab/cytoqc documentation built on Jan. 25, 2023, 11:05 p.m.