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