Splice event detection and quantification from RNA-seq data

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Documentation for package ‘SGSeq’ version 1.2.2

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A C E F G M P S T 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 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
countsTotal Accessing and replacing assay data
countsTotal-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
countsTotal<- Accessing and replacing assay data
countsTotal<--method Accessing and replacing assay data
countsVariant Accessing and replacing assay data
countsVariant-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
countsVariant<- Accessing and replacing assay data
countsVariant<--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
findSGVariants Find 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 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 library information from BAM files
getSGFeatureCounts Compatible counts for splice graph features from BAM files
getSGVariantCounts Representative counts and frequency estimates for splice variants

-- M --

makeSGFeatureCounts Create 'SGFeatureCounts' object
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 splice variant frequencies
predictTxFeatures Splice junction and exon prediction from BAM files
processTerminalExons Process predicted terminal exons

-- 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'
SGVariantCounts Constructor function for S4 class 'SGFeatureCounts'
SGVariants Constructor function for S4 class 'SGVariants'
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
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