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 |
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 |
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 |
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 |
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 |
mergeTxFeatures | Merge redundant features |
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 |
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 |
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 |
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 |