# Prediction, quantification and visualization of alternative transcript events from RNA-seq data

## Documentation for package ‘SGSeq’ version 1.0.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C E F G M P S T V

## -- A --

analyzeFeatures | Analysis of splice graph features from BAM files
analyzeVariants | Analysis of transcript variants
annotate | Annotation with respect to transcript features
assays | Accessing and replacing assay data

## -- C --

closed3p | Accessing and replacing column slots
closed3p-method | Accessing and replacing column slots
closed3p<- | Accessing and replacing column slots
closed3p<--method | Accessing and replacing column slots
closed5p | Accessing and replacing column slots
closed5p-method | Accessing and replacing column slots
closed5p<- | Accessing and replacing column slots
closed5p<--method | Accessing and replacing column slots
convertToSGFeatures | Convert transcript features to splice graph features
convertToTxFeatures | Convert to TxFeatures object
counts-method | Accessing and replacing assay data
counts<--method | Accessing and replacing assay data
countsTotal3p | Accessing and replacing assay data
countsTotal3p-method | Accessing and replacing assay data
countsTotal3p<- | Accessing and replacing assay data
countsTotal3p<--method | Accessing and replacing assay data
countsTotal5p | Accessing and replacing assay data
countsTotal5p-method | Accessing and replacing assay data
countsTotal5p<- | Accessing and replacing assay data
countsTotal5p<--method | Accessing and replacing assay data
countsVariant3p | Accessing and replacing assay data
countsVariant3p-method | Accessing and replacing assay data
countsVariant3p<- | Accessing and replacing assay data
countsVariant3p<--method | Accessing and replacing assay data
countsVariant5p | Accessing and replacing assay data
countsVariant5p-method | Accessing and replacing assay data
countsVariant5p<- | Accessing and replacing assay data
countsVariant5p<--method | Accessing and replacing assay data

## -- E --

eventID | Accessing and replacing column slots
eventID-method | Accessing and replacing column slots
eventID<- | Accessing and replacing column slots
eventID<--method | Accessing and replacing column slots
exportFeatures | Export to BED format

## -- F --

featureID | Accessing and replacing column slots
featureID-method | Accessing and replacing column slots
featureID3p | Accessing and replacing column slots
featureID3p-method | Accessing and replacing column slots
featureID3p<- | Accessing and replacing column slots
featureID3p<--method | Accessing and replacing column slots
featureID5p | Accessing and replacing column slots
featureID5p-method | Accessing and replacing column slots
featureID5p<- | Accessing and replacing column slots
featureID5p<--method | Accessing and replacing column slots
featureID<- | Accessing and replacing column slots
featureID<--method | Accessing and replacing column slots
filterTerminalExons | Filter terminal exons that share splice sites with internal exons
findTxVariants | Find transcript variants from splice graph
FPKM | Accessing and replacing assay data
FPKM-method | Accessing and replacing assay data
FPKM<- | Accessing and replacing assay data
FPKM<--method | Accessing and replacing assay data
from | Accessing and replacing column slots
from-method | Accessing and replacing column slots
from<- | Accessing and replacing column slots
from<--method | Accessing and replacing column slots

## -- G --

geneID | Accessing and replacing column slots
geneID-method | Accessing and replacing column slots
geneID<- | Accessing and replacing column slots
geneID<--method | Accessing and replacing column slots
geneName | Accessing and replacing column slots
geneName-method | Accessing and replacing column slots
geneName<- | Accessing and replacing column slots
geneName<--method | Accessing and replacing column slots
getBamInfo | Obtain alignment information from BAM files
getSGFeatureCounts | Compatible counts for splice graph features from BAM files
getTxVariantCounts | Representative counts and frequency estimates for transcript variants

## -- M --

mergeTxFeatures | Merge redundant features

## -- P --

plotFeatures | Plot splice graph and heatmap of expression values
plotSpliceGraph | Plot splice graph
plotVariants | Plot splice graph and heatmap of variant frequencies
predictTxFeatures | Transcript feature prediction from BAM files

## -- S --

segmentID | Accessing and replacing column slots
segmentID-method | Accessing and replacing column slots
segmentID<- | Accessing and replacing column slots
segmentID<--method | Accessing and replacing column slots
SGFeatureCounts | Constructor function for S4 class 'SGFeatureCounts'
SGFeatures | Constructor function for S4 class 'SGFeatures'
slots | Accessing and replacing column slots
splice3p | Accessing and replacing column slots
splice3p-method | Accessing and replacing column slots
splice3p<- | Accessing and replacing column slots
splice3p<--method | Accessing and replacing column slots
splice5p | Accessing and replacing column slots
splice5p-method | Accessing and replacing column slots
splice5p<- | Accessing and replacing column slots
splice5p<--method | Accessing and replacing column slots

## -- T --

to | Accessing and replacing column slots
to-method | Accessing and replacing column slots
to<- | Accessing and replacing column slots
to<--method | Accessing and replacing column slots
TxFeatures | Constructor function for S4 class 'TxFeatures'
txName | Accessing and replacing column slots
txName-method | Accessing and replacing column slots
txName<- | Accessing and replacing column slots
txName<--method | Accessing and replacing column slots
TxVariantCounts | Constructor function for S4 class 'SGFeatureCounts'
TxVariants | Constructor function for S4 class 'TxVariants'
type | Accessing and replacing column slots
type-method | Accessing and replacing column slots
type<- | Accessing and replacing column slots
type<--method | Accessing and replacing column slots

## -- V --

variantFreq | Accessing and replacing assay data
variantFreq-method | Accessing and replacing assay data
variantFreq<- | Accessing and replacing assay data
variantFreq<--method | Accessing and replacing assay data
variantID | Accessing and replacing column slots
variantID-method | Accessing and replacing column slots
variantID<- | Accessing and replacing column slots
variantID<--method | Accessing and replacing column slots
variantName | Accessing and replacing column slots
variantName-method | Accessing and replacing column slots
variantName<- | Accessing and replacing column slots
variantName<--method | Accessing and replacing column slots
variantType | Accessing and replacing column slots
variantType-method | Accessing and replacing column slots
variantType<- | Accessing and replacing column slots
variantType<--method | Accessing and replacing column slots