Annotation with respect to transcript features
Convert to TxFeatures object
Export to BED format
Annotate splice variants in terms of canonical events
Analysis of splice variants
Convert transcript features to splice graph features
Accessing and replacing assay data
Compatible fragment counts for exons
Analysis of splice graph features from BAM files
Filter predicted features
Compatible counts for splice graph features from BAM files
Obtain library information from BAM files
getSGFeatureCountsPerSample
Compatible fragment counts for splice graph features
Create SGFeatureCounts
object
Create interpretable splice variant names
Modified findOverlaps
function for IRanges
,
IRangesList
objects
Find splice variants from splice graph
Example region of interest
Compatible fragment counts for splice junctions
Remove exons with no flanking splice junctions
Example splice graph features
Example sample information
Accessing and replacing column slots
Identify splice junctions
IRanges
-based identification of splice junctions and exons
Process predicted terminal exons
predictTxFeaturesPerStrand
Identification of splice junctions and exons for a given
chromosome and strand
Example splice variants
Constructor function for S4 class SGFeatureCounts
predictCandidatesInternal
Identify candidate internal exons
predictCandidatesTerminal
Identify candidate terminal exons
Splice junction and exon prediction from BAM files
predictTxFeaturesPerSample
Identification of splice junctions and exons from BAM file
Constructor function for S4 class TxFeatures
Merge redundant features
Plot splice graph and heatmap of expression values
Constructor function for S4 class SGVariants
Example splice variant counts
Plot splice graph
Plot splice graph and heatmap of splice variant frequencies
Constructor function for S4 class SGFeatures
Constructor function for S4 class SGSegments
Representative counts and frequency estimates for
splice variants
Example transcript features
Identify terminal exons
Identify internal exons
Example splice graph feature counts
Compatible fragment counts for splice sites
Constructor function for S4 class SGFeatureCounts