scaled_aof_score: Calculates scaled aof scores and sample quality scores

In prybakowska/CytoQP: Cytometry data quality control and cleaninig

Calculates scaled aof scores and sample quality scores

Description

Calculates scaled AOF scores and sample quality score. Additionally plots heatmaps for both raw aof scores and scaled aof scores.

Usage

scaled_aof_score(aof_scores, out_dir = NULL, aof_channels = NULL, batch = NULL)

Arguments

aof_scores	Matrix, array, Aof scores obtained using function cytutils::greedyCytometryAof.
out_dir	Character, pathway to where the plots and scores should be saved, if NULL file.path(getwd(), "Quality_Control) will be used.
aof_channels	Character vector with the markers and their corresponding channel names used for aof_scoring. Used only for plotting markers instead of channels. If NULL (default) the colnames(aof_scores) will be used.
batch	Character, acquisition batch for each fcs file. Pass to FlowSOM plot name, default is set to NULL be saved, default is set to working directory.

Value

Returns data frame with sample scores.Saved heatmaps and data frames for AOF scores and AOF scaled scores.

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