johanneskersting/dsstatistics

Differential Splicing Statistics

The repository contains two scripts:

• functions_ds.R: A R-script containing all functions necessary for the evaluation.
• plots_ds.Rmd: A R-notebook which calls theses functions and is used for visualization.

Both files should be located in the same directory to work properly.

Usage

functions_ds.R provides the following functions:

For reading the groundtruth:

• read_info(path): Takes a path to the info file generated by the AS-Simulator and reads it.
• read_annotation(path): Takes a path to the annotation file generated by the AS-Simulator and reads it.
• load_introns(read_annotation_output,TxDb): Takes the object returned by read_annotation and the genome annotatoin (as TxDb object) and creates additional event location annotations.

For processing the different tool outputs:

• read_ds(path,tool): Takes a path to the output directory of a tool and the tool name to read its output.
• pre_filter_type(read_ds_output,read_info_output): Takes a parsed tool output and the read info, to remove events and gene with unknown types.
• count_ds(read_ds_output,tool,...): Takes a parsed tool output (potentially filtered by pre_filter_type) to count tp, fp, fn for three different levels, which get returned as a data.table.

Supported tool names for the functions read_ds and count_ds are:

cash, eventpointer, aspli, majiq, spladder, edger, psisigma and junctionseq

The names are used to call the right parser internally.

Plotting

plots_ds.Rmd can be used to visualize the results.

Required libraries

The scripts utilize the following R libraries:

• data.table
• ggplot2
• tidyr
• GenomicRanges
• GenomicFeatures
• stringr