PeacoQC-class: S4 PeacoQC Class

In CytobankAPI: Cytobank API Wrapper for R

S4 PeacoQC Class

Description

A PeacoQC object that holds pertinent PeacoQC data QC run information This class should never be called explicitly. If a user would like to create a new Cytobank PeacoQC object, utilize the peacoqc.new function, or any other PeacoQC endpoints that return PeacoQC objects documented in the 'Details' section.

Value

A PeacoQC object

Slots

author

character representing the author of the PeacoQC analysis

attachment_id

numeric representing the PeacoQC attachment to the source experiment containing the PeacoQC results

channel_unique_identifiers

list of character representing a list of unique channel identifiers

compensation_id

the compensation ID selected for the PeacoQC data QC

completed

logical representing whether or not the PeacoQC is complete

consecutive_bins

numeric if 'good' bins are located between bins that are removed, they will also be marked as 'bad'. Can be set to any integer between 1 and 50 (inclusive)

detection_method

character representing the method(s) used to detect and filter out anomalies. - choose from the following : ("all" [default], "IT", "MAD")

errors

list of character representing a list of error messages of the PeacoQC

failed

logical representing whether or not the PeacoQC is failed

fcs_files

list of integers or character representing a list of FCS file IDs

final_result

character representing whether or not the PeacoQC is successful

heatmap_attachment_id

numeric representing the PeacoQC heatmap image attachment to the source experiment

it_limit

numeric representing the IsolationTree parameter. Higher values mean the IT method will be less strict. Can be set to any float between 0.2 and 1.0(inclusive)

mad

numeric representing the MAD parameter. Higher values mean the MAD method will be less strict. Can be set to any integer between 1 and 100 (inclusive)

max_bins

numeric representing the maximum number of bins that can be used in the cleaning process. If this value is lowered, larger bins will be made. Can be set to any integer between 40 and 1,000,000 (inclusive)

name

the name of the advanced analysis

peaco_qc_id

numeric representing the PeacoQC ID

remove_margins

if the value is true, they will remove margin events based on the internal description of the fcs file. Can be set to a boolean value

source_experiment

the source experiment ID the advanced analysis is associated with

status

character representing the status of the advanced analysis

type

character

use_internal_scales_for_margins

logical this parameter is required when removeMargins is set to true. Set to true, the events will transtorm with fcs file internal scales. Set to false, the events will transform with cytobank scales. Can be set to a boolean value

validFcsFileIds

list of integers or character representing a list of valid FCS file IDs can run PeacoQC

CytobankAPI documentation built on April 21, 2023, 9:08 a.m.