process.pH.induction: Processes a flow dataset of induction timeseries

In ctriandafillou/flownalysis: Analysis of Yeast Protein Induction and pH by Flow Cytometry

Description

This function takes a dataframe produced by merge_flowSet and produces a processed dataframe with induction data; currently requires pre-classification of populations into a column called 'population' Remaining to do: 1. generate calibration curve and convert to pH within function; 2. find a way to change the induction channel name;

Usage

process.pH.induction(df, cc = FALSE, summarise = FALSE,
  ref.strain = "ycgt028", ref.background = "media")

Arguments

df	The dataframe containing the raw induction data. Identifier column should be called 'exp' and formatted as background data: 'controls_strain_background.fcs'; or induction data: 'timepoint_treatment_fitness_pH.fcs'
cc	whether or not to generate a calibration curve and calculate intracellular pH; default is FALSE : CURRENTLY UNAVAILABLE
ref.strain	the reference strain; default is "ycgt028"
ref.background	the background of the reference strain; default is "media"
summarize	function returns either a median-summarised timeseries (TRUE) or unsummarized data (FALSE; default)
channel	induction channel name; default is "PEDazzle.A" : CURRENTLY UNAVAILABLE

Value

processed dataframe

ctriandafillou/flownalysis documentation built on Sept. 7, 2020, 1:48 a.m.