Splice event prediction and quantification from RNA-seq data

[Up] [Top]

Documentation for package ‘SGSeq’ version 1.26.0

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