process_cell_data: Process raw cell data

In SciOmicsLab/PhenoComb: Phenotype Combinatorial Analysis

Process raw cell data

Description

process_cell_data uses the channel_data and sample_data to filter columns and cells from cell_data and discretize values based on thresholds defined on channel_data.

Usage

process_cell_data(
  cell_data,
  channel_data,
  sample_data,
  sampleID_col = "Sample_ID",
  n_threads = 1
)

Arguments

cell_data	Data.Frame where each column is a channel of measurement plus one column with sample IDs. Each row is a cell.
channel_data	Data.Frame containing columns named: Channel, Marker, T1, [T2, T3, ... , Tn], [OOB].
sample_data	Data.Frame containing a Sample_ID column and additional grouping columns for the samples.
n_threads	Number of threads to be used (Only useful if there is an OOB column in channel_data). Default: 1
sample_ID_col	Name of the column in cell_data where the Sample IDs are stored. Default: "Sample_ID"

Value

Data.Frame with filtered and discretized cells.

SciOmicsLab/PhenoComb documentation built on Aug. 26, 2023, 1:28 p.m.