Differential Expression Analysis of RNA-Seq Data

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Documentation for package ‘diffwrap’ version 0.6-3

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

Help Pages

correlogram_pheatmap	Function to create a correlogram pheatmap, i.e., a plot to check randomness in the data set.
diffExpr	Main wrapper for executing the entire pipeline from reading in expression data such as count files to producing text files and graphs
diffr_expr_generate_cleaned_de_table_output	Helper function to generate an output table with only most relevant columns
diffr_pheatmap	Function to create a heatmap from differential gene expression values
diffr_venn	Function to produce a Venn diagram of differentially expressed gene tables
diffwrap	Differential expression analysis of RNA-Seq data
diffwrap_counts	Simulated RNA-Seq read counts for the package examples
diffwrap_samp_info	Sample sheet accompanying the simulated example counts
diff_expr_3d_scatterplot	Function to generate a 3D scatterplot
diff_expr_biomart	Function to retrieve additional information from biomart
diff_expr_dendro_plot	Function to generate dendrogram plots based on hierarchical clustering
diff_expr_extract_contrasts	Function to extract contrasts and generate top tables and plots
diff_expr_filter_counts	Function to filter counts
diff_expr_fit	Function to compute linear model fit and optionally apply 'voom' beforehand
diff_expr_get_samp_info	Function to standardize samp.info sample information data frame
diff_expr_ggplot_mds	Function to generate a MDS plot using 'ggplot2'
diff_expr_make_contrasts	Function to make contrast matrix
diff_expr_make_design	Function to create design matrix
diff_expr_ma_plot	Function to generate a M-A plot using 'ggplot2'
diff_expr_mds_plot	Wrapper around 'limma::plotMDS' to generate a MDS plot
diff_expr_PCA	Function to do PCA using 'stats::prcomp'
diff_expr_PCA_ggbiplot	Function to generate a PCA biplot using 'ggbiplot.n', a version of 'ggbiplot' from https://github.com/vqv/ggbiplot.
diff_expr_PCA_ggplot	Function to generate an ordinary two-dimensional PCA plot using 'ggplot2'
diff_expr_pseudo_counts	Function to calculate pseudo counts representing batch-corrected normalised but untransformed values
diff_expr_pval_hist_plot	Function to generate a histogram of the P-Value distribution
diff_expr_QC_plots	Main wrapper function for QC plots
diff_expr_read_counts	Function to read counts as produced by htseq-count
diff_expr_volcano_plot	Function to generate a Volcano plot using 'ggplot2'
format_ensembl_ids_annotated_to_term	Helper function for formatting the gene ID column of enrichment data frame.
get_hm_breaks	Function to define breaks to be used for changing the palette of the heatmap.
get_hm_colors	Function to compute colour palettes to be used in the heatmap.
ggbiplot.n	Make a biplot of PCA output data using ggplot2.
make_pheatmap_anno_color	Function to create the annotation colour list used in the heatmap
pheatmap_plots	Function to generate heatmap of gene expression values
plot_enrichment_network	Function for making network visualisation based on enrichment result, DE gene table and thresholding. Can take the input tables either as data frames or Excel files
prepare_scale_for_legend	Helper function for enrichment visualisations: prepare plot legend y coordinates and labels
prepare_volcano_of_given_property	Helper function that returns a volcano plot.
quantile_breaks	Function to define quantile breaks to be used for changing the palette of the heatmap.
reorderFactors	Function which reorders the levels of a column of a data frame specified as a factor
run.topGO	Function to run GO term enrichment analysis using the 'topGO' package.
runEnrichmentAnalyses	Wrapper for executing various enrichment analyses
run_clusterProfiler_GO	Runs clusterProfiler GO enrichment function for a DEG list or for a ranked gene list.
run_clusterProfiler_KEGG	Runs clusterProfiler KEGG enrichment function for a DEG list or for a ranked gene list.
run_gprofiler	Runs gprofiler function for a DEG list or for a ranked gene list.