# "Useful utility functions used at the core"

## Documentation for package ‘CHBUtils’ version 0.1

- DESCRIPTION file.

## Help Pages

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