Splice event prediction and quantification from RNA-seq data

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Documentation for package ‘SGSeq’ version 1.42.1

• 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