electrophoresis: Electrophoresis class

In jwfoley/bioanalyzeR: Analysis of Agilent electrophoresis data

Electrophoresis class

Description

This S3 class is a generic container for electrophoresis data and metadata. The constructor simply assembles the provided members into a class structure without checking them: if they are formatted incorrectly there will be no warnings at this stage.

Usage

electrophoresis(
  data = NULL,
  assay.info = NULL,
  samples = NULL,
  peaks = NULL,
  regions = NULL,
  mobility.functions = NULL
)

Arguments

data	A tall data frame of the run data, specifically: time (Bioanalyzer, ProSize) - time when this data point was measured aligned.time (Bioanalyzer, ProSize) - measurement time aligned between the expected times of the marker peaks distance (TapeStation) - migration distance of the measurement from the top of the gel area relative.distance (TapeStation) - migration distance normalized relative to the marker peaks fluorescence - fluorescence reading at this point length - estimated molecule length at this point concentration - estimated concentration of the area under the curve between this point and the previous one molarity - estimated molarity of the area under the curve between this point and the previous one
assay.info	A list of metadata about each batch and the assay kit used.
samples	A data frame of metadata for each sample (also annotated to data, peaks, and regions with the same factor levels), specifically: batch - the batch (instrument run) of the sample, from the file name well.number - the well number in which the sample was loaded sample.name - the name of the sample sample.observations - notes about this sample supplied by the user or the Agilent software sample.comment - notes about this sample supplied by the user reagent.id (TapeStation) - the name of the ScreenTape used for this sample ladder.well - which well contains the ladder that calibrates this sample RIN, DIN, RQN, ⁠28S/18S⁠, etc. - sample quality metrics reported by the Agilent software
peaks	A data frame of peaks reported by the Agilent software, annotated with their lower and upper boundaries in various scales.
regions	A data frame of regions of interest reported by the Agilent software, annotated with their lower and upper boundaries in varous scales.
mobility.functions	A list of model functions, one per ladder used for calibration, to convert migration speed measurements (aligned time or relative distance) into estimated molecule lengths.

jwfoley/bioanalyzeR documentation built on Aug. 1, 2023, 4:46 a.m.