![]() ![]() The treatment whose name matches the string is the universalĭata frame: Use when more than one negative control exists, and you String: Use when a single set of observations is a universal control. Observations will be the negative controls. Each treatment mustĬontain one or more observations with this concentration, and these (typically 0) that indicates the vehicle control. Number: Use when each treatment has been labeled with a concentration Of the column named 'value_normalized' will be copied from the contents of NA: Use when there are no negative control measurements. Defaults to "plate_1".Ĭontrols the normalization. Text string identifying this experiment, useful if write_platemap_to_XML: Write a loaded plate map object in XML formatĬreate_dataset ( sample_types, treatments, concentrations, values, hours = 0, plate_id = "plate_1", negative_control = NA, summary_method = "mean" ).timecourse_relative_grid: Calculate fold-change in Dose Response Curve AUC and EC50 at.timecourse_AUC_ratio: Calculate AUC for sample/treatment at a concentration across.synergy_interaction_CI: Construct confidence intervals for observed effects at.synergy_bliss: Construct synergy matrix of values expected from Bliss.summary.HT_fit: Summarize the results of a dose response fit.standardize_treatment_assigments: Make two treatments consistently assigned to either treatment.read_plates_from_Incucyte_export: Read Incucyte-formatted Excel document for a plate at one or.read_platemap_from_Incucyte_XML: Read plate maps from Incucyte plate map XML extract.read_platemap_from_excel: Read plate maps into a list of three data frames.read_dataset: Read a dataset from a text file.plot_values_by_plate: Plot an image of the raw intensities for a plate.plot_timecourse_raw: Plot an time course of the raw intensities.plot_synergy_median_effect: plot FA vs.plot_synergy_interaction_index: Plot interaction index with confidence intervals for observed.plot.HT_fit: Plot a dose response curve from a HTfit object.plot_fit_statistic: Plot a dose response curve summary values across one or more.plot_color_grid: Plot a grid of colors given a matrix of numbers.metric_to_grid: reshape a set of values to a matrix with axes defined by X.get_treatments: Sorted unique list of treatments.get_sample_types: Sorted unique list of sample types.get_hours: Sorted unique list of hours since time zero.get_concentrations: Sorted unique list of treatment concentrations.fit_statistics_matrixes: Convert fit statistics data frame to matrixes for further.fit_statistics: Fit all observations and return summary information from.fit_DRC: Attempt to fit a dose-response curve from the dataset and.create_synergy_dataset: Create a synergy dataset from raw data without a plate map.create_empty_plate_map: Create an empty plate map. ![]() ![]() create_empty_plate: Create a plate list with empty elements.create_dataset: Create a dataset from raw data without a plate map.convert_to_foldchange: Convert values in M1, M2 to fold-change M1 vs M2.combine_data_and_map: Combine raw data and plate map to produce a single tall data.chou_synergy_CI_median: Plot single-value Chou Combination Index at IC50.chou_synergy: Calculate statistics needed for Chou Synergy Curve fitting is.boxplot_label_outliers: Standard boxplot with labeled outliers. ![]()
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