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SGSeq (version 1.2.2)

Splice event detection and quantification from RNA-seq data

Description

Predict splice junctions and exons from BAM files and obtain compatible read counts and FPKMs. Identify splice events and estimate relative usage of splice variants based on compatible read counts at event boundaries.

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Version

Version

1.2.2

License

Artistic-2.0

Maintainer

Leonard Goldstein

Last Published

February 15th, 2017

Functions in SGSeq (1.2.2)

Annotation with respect to transcript features

convertToTxFeatures

Convert to TxFeatures object

Export to BED format

annotateSGVariants

Annotate splice variants in terms of canonical events

analyzeVariants

Analysis of splice variants

convertToSGFeatures

Convert transcript features to splice graph features

Accessing and replacing assay data

Compatible fragment counts for exons

analyzeFeatures

Analysis of splice graph features from BAM files

Filter predicted features

getSGFeatureCounts

Compatible counts for splice graph features from BAM files

Obtain library information from BAM files

getSGFeatureCountsPerSample

Compatible fragment counts for splice graph features

makeSGFeatureCounts

Create SGFeatureCounts object

makeVariantNames

Create interpretable splice variant names

findOverlapsRanges

Modified findOverlaps function for IRanges, IRangesList objects

Find splice variants from splice graph

Example region of interest

junctionCompatible

Compatible fragment counts for splice junctions

removeExonsIsolated

Remove exons with no flanking splice junctions

Example splice graph features

Example sample information

Accessing and replacing column slots

predictJunctions

Identify splice junctions

IRanges-based identification of splice junctions and exons

processTerminalExons

Process predicted terminal exons

predictTxFeaturesPerStrand

Identification of splice junctions and exons for a given chromosome and strand

Example splice variants

SGVariantCounts

Constructor function for S4 class SGFeatureCounts

predictCandidatesInternal

Identify candidate internal exons

predictCandidatesTerminal

Identify candidate terminal exons

predictTxFeatures

Splice junction and exon prediction from BAM files

predictTxFeaturesPerSample

Identification of splice junctions and exons from BAM file

Constructor function for S4 class TxFeatures

mergeTxFeatures

Merge redundant features

Plot splice graph and heatmap of expression values

Constructor function for S4 class SGVariants

Example splice variant counts

plotSpliceGraph

Plot splice graph

Plot splice graph and heatmap of splice variant frequencies

Constructor function for S4 class SGFeatures

Constructor function for S4 class SGSegments

getSGVariantCounts

Representative counts and frequency estimates for splice variants

Example transcript features

predictExonsTerminal

Identify terminal exons

predictExonsInternal

Identify internal exons

Example splice graph feature counts

splicesiteOverlap

Compatible fragment counts for splice sites

SGFeatureCounts

Constructor function for S4 class SGFeatureCounts