/RT-CETSA-Analysis

Primary LanguageRMIT LicenseMIT

RT-CETSA R Analysis

Packages Needed:

-library(tidyverse) -library(drc) -library(stringr) -library(readxl) -library(stringr) -library(ggthemes) -library(cowplot) -library(hrbrthemes) -library(ggpubr)

Functions List:

  • construct_grid(row_num = 16, col_num = 24, pad_num = FALSE)

    • Construct grid with the option for headers compatible with moltenprot

  • prepMatLabforMolt(file_loc = './data/rtcetsa_raw.xlsx', sheet = 'Sheet1', col_names = FALSE,start_temp = 37, end_temp = 90)

    • Read in MatLab file and construct back to appropriate plate format.

  • retrieveMoltenData(model = 'standard', plate_format = 384)

    • Takes in moltenprot files and reconstructs according to input model. Need to expand for other types.

  • retrieve_FittedCurves(model = 'baseline-fit', start_temp = 37, end_temp = 90)

    • Gather base-line corrected fit curves for the 384-well plate and pivot plate
    • model = c('fit_curves','baseline-fit')
      • fit_curves: Curve fitting to cleaned raw data
      • baseline-fit: Baseline correction and normalization to [0-1].

  • bind_fulldf(param_df, curve_df)

    • Construct full data frame with curve fit and parameters for analysis

  • kelToCel(df)

    • Convert any columns containing Kelvin values from MoltenProt to Celsius

  • add_tempheaders(df, start_temp = 37,end_temp = 90)

  • add_rowcol(df, well_num)

  • well_assignment()

    • Process temperature headers coming from moltenprot.

  • plate_assignment()

    • Bring in platemaps to assign concentration and id to wells. Plate maps need to follow a specific format found in the template file.

  • calculate_auc(df)

    • Calculates AUC from curve fit data at each temperature for each well.

  • control_grouping(df, control = 'DMSO')

    • Creates a df using input control wells

  • control_variability(df)

    • Reads out control group variability

  • control_thermogram()

    • Output control group thermogram and %CV.

  • dr_fit()

  • dr_analysis()

  • plate_heatmap()

  • export_heatmaps()

  • dmso_rss()

  • compare_models()

  • calculate_meltingparams()

    • Takes full_df and returns the melting curve parameters derived from MoltenProt after subtracting the vehicle control from each well.

  • plot_volcanos()

  • parameter_doseresponse()

  • calculate_zscore()

  • convert_zscore()

  • fit_nullmodel()

  • fit_altmodel()

  • compute.rss.models()

  • compute_parameter.rssmodel()

  • dr.thermogram()