A Transparent Analysis Pipeline for Mammalian Metabolic Phenotype Microarray Data

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Documentation for package ‘MetPhenoR’ version 1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotate_chemical	Annotate assay data with chemical identities
annotate_metadata	Annotate assay data with metadata
classify_growth_curve_types	Classify Growth Curve Dynamics
compute_auc_ci	Estimate Area Under the Curve (AUC) with Bootstrap Confidence Intervals
compute_auc_ratio	Compute AUC Ratio Relative to Controls
filter_data	Exclude 96-well plate
PlateInfo	An example '..._PlateInfo.csv" file
plot_auc	Plot AUC Profiles by Plate and Experimental Conditions
plot_auc_ratio_by_group	Plot AUC ratio heatmap by group
plot_auc_ratio_heatmap	Plot AUC ratio heatmap
plot_auc_ratio_violin	Plot AUC ratio distribution as violin plots
plot_controls_tween_all_plate	Plot Controls vs Tween Across All Plates (with Control Reference Range)
plot_controls_tween_per_plate	AUC Plot for Controls and Tween Compounds within plate
plot_growth_curve	Visualize Growth Curves and Plate Layouts from Classified Data
plot_latest_timepoint	Plot Final Time Point per Experimental Condition
PM_M01_M02	Annotations for metabolic plates PM-M01 and PM-M02
PM_M11_M14	Annotations for anti-cancer drug plates PM-M11 to PM-M14
processed_data	Example data set as result of read_folder.R with sample_column = "Sample" and variables = c("cell.line", "LKB1.status", "radiation.dose")
qc_data	Quality Control for input data after noise correction
RawRead	Example Raw Read from Odin Biolog
read_folder	Process CSV Plate Data stored in folder into data frame in long format