"Useful utility functions used at the core"

Documentation for package ‘CHBUtils’ version 0.1

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chb_utils-package	chb_utils
annotate_df	Annotate Dataframe containing Ensembl IDs with Gene Symbols and Descriptions
boxplotoutliers	Cel file IDs of intensity boxplot outlier arrays (in characters).
chb_utils	chb_utils
col2rownames	add a column to a dataframe consisting of the current rownames
convertIDs	Get other Ids for genes in the same order
create_report	Create report of QC
getTFpairs	Get mouse TF-target pairs from opossum database
get_biomart	Get biomart annotation from id
ggheatmap	generate a heatmap + dendrograms, ggplot2 style
ggheatmap.show	Display a ggheatmap
ggplotDispEsts	Plot Dispersion Estimates - nicer ggplot version of DESeq graph
mds	Plot MDS
mdsplot.RGset	MDS (MultiDimensional Scaling) Plots
nuseoutliers	Cel file IDs of intensity NUSE outlier arrays (in characters).
PCAplot.cds	Pairwise Principal Component Analysis Plots of CountDataSet objects
PCAplot.eset	Pairwise Principal Component Analysis Plots
plotDE	Plots the differntially expressed genes on an MA plot, ggplot style If adjusted pvalues are present, colors those that pass cutoff red
plot_dendro	ggplot based dendrogram plot
print_enrichGO	Clean and print results from enrichGO
qqplot_JH	Plots the pvalue quantiles against the uniform distribution. If adjusted pvalues are present, colors those that pass cutoff red
rleoutliers	Cel file IDs of intensity RLE outlier arrays (in characters).
row2colnames	add a column to a dataframe consisting of the current rownames
runGO	Run GO using clusterprofiler
variance_by_component	Plot PC importance
volcano_density_plot	Create volcano plot from log2FC and adjusted pvalues data frame
write_report	Write report of QC