README.md

In PNorvaisas/PFun: Framework For HT Workflows

PFun

Collection of useful functions employed in data analysis

• adjustments - Calculates FDR for each contrast and adds p-Stars
• contrast.adjust - Adjust contrasts when there is an interaction between group and H0: group_difference!=0
• clustorder - Orders factor levels using hierarchical clustering
• covariation - Calculates covariation between contrasts and estimates this correlation linear regression parameters
• enrichment - Calculates enrichment using hypergeometric test
• getellipse - Generates SD ellipses
• getresults - Generates LM and Tukey-HSD results using hypothesise output
• group.filter - Filters experimental groups in EdgeR
• HMap - Draw heatmap using ggplot2
• lmtest - Quick way to perform 1-way/2-way ANOVA analysis
• hypothesise - Applies Tukey's HSD based on provided contrasts for experimental groups in LM fit object
• MinMeanSDMax - Generates Min, Mean, SD, Max values of data vector for ggplot boxplots
• multiplex - Generates multidimensional pair-wise comparison table
• pStars - Generates clean p-Stars
• PlotEnrichment - Plots enrichment heatmap
• PCAprep - PCA analysis results for standardised plotting
• pStars - Generates p-Stars
• read.contrasts - Contrast table reader
• theme_Heatmap.R - ggplot2 heatmap theme
• theme_PN - Custom ggplot2 theme
• theme_Publication - Custom publication friendly ggplot2 theme

PNorvaisas/PFun documentation built on May 20, 2019, 4:13 p.m.