README.md

In MDegener/SpliceSelector: Filtering of Results from common Alternative Splicing Software

SpliceSelector Tool

The SpliceSelector package faclitates a targeted analysis of alternatively spliced candidate exons in any RNAseq dataset. The required input will be a list of genomic coordinates (chr:start-end), an exon annotation file (e.g. GENCODE) and the results from common splicing analysis tools. Results from MISO, DEXSeq, leafcutter and MAJIQ will be supported.

Development state

Currently, only the following helper functions have been implemented:

1. liftOverGRange.R

• wrapper function for UCSC's liftOver tool
• usage: liftOverGRange(grObject, givenAssembly, targetAssembly, libPath)
• converts coordinates in genomic range object from the given assembly to the target assembly
• liftOver chain is stored under libPath

2. getOverlap.R

• compares query coordinates with coordinates from a .gtf/.gff exon annotation file (e.g. GENCODE)
• creates a table listing all overlapping coordinates with their corresponding overlap type
• usage: getOverlap(grObject, exonAnnotation)
• grObject is a genomic range object that can be generated with rtracklayer and contains the query coordinates
• overlap types:
  • "equal" - perfect match of start and end positions
  • "within" - query coordinates that fall within annotation coordinates of an exon
  • "spans one" - query coordinates that span annotation coordinates of one exon
  • "spans multiple" - query coordinates that span annotation coordinates of multiple exons
  • "none" - query coordinates that do not match to any exon in annotation coordinates
  • "other" - any type of overlap that is not covered by the other categories

3. plotOverlapOverview.R

• plots results of getOverlap.R script in two barplots
• usage: plotOverlapOverview(overlap, plotPrefix, outDir)

4. getBiomaRtAnnotation

• wrapper function for querying BioMart Ensembl database to extract gene annotation (e.g. coordinates, description)
• usage: getBiomaRtAnnotation(identifierList, identifierType, species)

5. createUCSCtrack

• creates a custom UCSC track from a genomic range object to view supplied coordinates in the UCSC genome browser
• usage: createUCSCtrack(grObject, outFile, trackName, trackDescription)

MDegener/SpliceSelector documentation built on Dec. 31, 2020, 2:18 p.m.