# Splice event prediction and quantification from RNA-seq data

## Documentation for package ‘SGSeq’ version 1.20.0

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

## Help Pages

A C E F G I M P S T U V

## -- A --

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

## -- C --

closed3p | Accessing and replacing metadata columns
closed3p-method | Accessing and replacing metadata columns
closed3p<- | Accessing and replacing metadata columns
closed3p<--method | Accessing and replacing metadata columns
closed3pEvent | Accessing and replacing metadata columns
closed3pEvent-method | Accessing and replacing metadata columns
closed3pEvent<- | Accessing and replacing metadata columns
closed3pEvent<--method | Accessing and replacing metadata columns
closed5p | Accessing and replacing metadata columns
closed5p-method | Accessing and replacing metadata columns
closed5p<- | Accessing and replacing metadata columns
closed5p<--method | Accessing and replacing metadata columns
closed5pEvent | Accessing and replacing metadata columns
closed5pEvent-method | Accessing and replacing metadata columns
closed5pEvent<- | Accessing and replacing metadata columns
closed5pEvent<--method | Accessing and replacing metadata columns
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

## -- E --

eventID | Accessing and replacing metadata columns
eventID-method | Accessing and replacing metadata columns
eventID<- | Accessing and replacing metadata columns
eventID<--method | Accessing and replacing metadata columns
exportFeatures | Export to BED format

## -- F --

featureID | Accessing and replacing metadata columns
featureID-method | Accessing and replacing metadata columns
featureID3p | Accessing and replacing metadata columns
featureID3p-method | Accessing and replacing metadata columns
featureID3p<- | Accessing and replacing metadata columns
featureID3p<--method | Accessing and replacing metadata columns
featureID3pEvent | Accessing and replacing metadata columns
featureID3pEvent-method | Accessing and replacing metadata columns
featureID3pEvent<- | Accessing and replacing metadata columns
featureID3pEvent<--method | Accessing and replacing metadata columns
featureID5p | Accessing and replacing metadata columns
featureID5p-method | Accessing and replacing metadata columns
featureID5p<- | Accessing and replacing metadata columns
featureID5p<--method | Accessing and replacing metadata columns
featureID5pEvent | Accessing and replacing metadata columns
featureID5pEvent-method | Accessing and replacing metadata columns
featureID5pEvent<- | Accessing and replacing metadata columns
featureID5pEvent<--method | Accessing and replacing metadata columns
featureID<- | Accessing and replacing metadata columns
featureID<--method | Accessing and replacing metadata columns
findSGVariants | Identify splice 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-method | Accessing and replacing metadata columns
from<- | Accessing and replacing metadata columns
from<--method | Accessing and replacing metadata columns

## -- G --

geneID | Accessing and replacing metadata columns
geneID-method | Accessing and replacing metadata columns
geneID<- | Accessing and replacing metadata columns
geneID<--method | Accessing and replacing metadata columns
geneName | Accessing and replacing metadata columns
geneName-method | Accessing and replacing metadata columns
geneName<- | Accessing and replacing metadata columns
geneName<--method | Accessing and replacing metadata columns
getBamInfo | Obtain library information from BAM files
getSGFeatureCounts | Compatible counts for splice graph features from BAM files
getSGVariantCounts | Representative counts and frequency estimates for splice variants

## -- I --

importTranscripts | Import transcripts from GFF file

## -- M --

makeSGFeatureCounts | Create 'SGFeatureCounts' object
mergeTxFeatures | Merge redundant features

## -- P --

plotCoverage | Plot read coverage and splice junction read counts
plotFeatures | Plot splice graph and heatmap of expression values
plotSpliceGraph | Plot splice graph
plotVariants | Plot splice graph and heatmap of splice variant frequencies
predictTxFeatures | Splice junction and exon prediction from BAM files
predictVariantEffects | Predict the effect of splice variants on protein-coding transcripts
processTerminalExons | Process predicted terminal exons

## -- S --

segmentID | Accessing and replacing metadata columns
segmentID-method | Accessing and replacing metadata columns
segmentID<- | Accessing and replacing metadata columns
segmentID<--method | Accessing and replacing metadata columns
SGFeatureCounts | Splice graph feature counts
SGFeatures | Splice graph features
SGVariantCounts | Splice graph variant counts
SGVariants | Splice graph variants
slots | Accessing and replacing metadata columns
splice3p | Accessing and replacing metadata columns
splice3p-method | Accessing and replacing metadata columns
splice3p<- | Accessing and replacing metadata columns
splice3p<--method | Accessing and replacing metadata columns
splice5p | Accessing and replacing metadata columns
splice5p-method | Accessing and replacing metadata columns
splice5p<- | Accessing and replacing metadata columns
splice5p<--method | Accessing and replacing metadata columns

## -- T --

to-method | Accessing and replacing metadata columns
to<- | Accessing and replacing metadata columns
to<--method | Accessing and replacing metadata columns
TxFeatures | Transcript features
txName | Accessing and replacing metadata columns
txName-method | Accessing and replacing metadata columns
txName<- | Accessing and replacing metadata columns
txName<--method | Accessing and replacing metadata columns
type-method | Accessing and replacing metadata columns
type<- | Accessing and replacing metadata columns
type<--method | Accessing and replacing metadata columns

## -- U --

updateObject | Update object
updateObject-method | Update object

## -- 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 metadata columns
variantID-method | Accessing and replacing metadata columns
variantID<- | Accessing and replacing metadata columns
variantID<--method | Accessing and replacing metadata columns
variantName | Accessing and replacing metadata columns
variantName-method | Accessing and replacing metadata columns
variantName<- | Accessing and replacing metadata columns
variantName<--method | Accessing and replacing metadata columns
variantType | Accessing and replacing metadata columns
variantType-method | Accessing and replacing metadata columns
variantType<- | Accessing and replacing metadata columns
variantType<--method | Accessing and replacing metadata columns