aof_scoring: Calculates AOF scores and scaled AOF scores

In prybakowska/CytoQP: Cytometry data quality control and cleaninig

Calculates AOF scores and scaled AOF scores

Description

Calculates AOF (Average Overlap Frequency) scores using flowSOM object and greedy algorithm from cytutils package.

Usage

aof_scoring(
  fcs_files,
  phenotyping_markers,
  markers_to_score,
  fsom,
  out_dir = NULL,
  batch = NULL
)

Arguments

fcs_files	Character, full path to fcs_files.
phenotyping_markers	Character vector, marker names to be used for clustering, can be full marker name e.g. "CD45" or "CD" if all CD-markers needs to be plotted.
fsom	FlowSOM object as generated by fsom_aof
out_dir	Character, pathway to where the AOF scores and plots should be saved, default is set to file.path(getwd(), "Quality_Control")
batch	Character, acquisition batch for each fcs file. This argument is passed to AOF plot names, default is set to NULL.

Value

Returns data frame with the scaled AOF scores and heatmap plots representing AOF scores and scaled AOF scores.

prybakowska/CytoQP documentation built on June 28, 2022, 12:36 a.m.