SGSeq package - RDocumentation

convertToTxFeatures

Convert to TxFeatures object

assays

Accessing and replacing assay data

exonCompatible

Compatible fragment counts for exons

exportFeatures

Export to BED format

filterFeatures

Filter predicted features

annotateSGVariants

Annotate splice variants in terms of canonical events

analyzeVariants

Analysis of splice variants

convertToSGFeatures

Convert transcript features to splice graph features

analyzeFeatures

Analysis of splice graph features from BAM files

annotate

Annotation with respect to transcript features

getSGFeatureCountsPerSample

Compatible fragment counts for splice graph features

getSGVariantCounts

Representative counts and frequency estimates for splice variants

findOverlapsRanges

Modified findOverlaps function for IRanges, IRangesList objects

getBamInfo

Obtain library information from BAM files

importTranscripts

Import transcripts from GFF file

findSGVariants

Find splice variants from splice graph

gr

Example genomic region of interest

getSGFeatureCounts

Compatible counts for splice graph features from BAM files

junctionCompatible

Compatible fragment counts for splice junctions

makeSGFeatureCounts

Create SGFeatureCounts object

makeVariantNames

Create interpretable splice variant names

mergeTxFeatures

Merge redundant features

predictCandidatesTerminal

Identify candidate terminal exons

predictCandidatesInternal

Identify candidate internal exons

plotSpliceGraph

Plot splice graph

plotVariants

Plot splice graph and heatmap of splice variant frequencies

predictExonsInternal

Identify internal exons

predictExonsTerminal

Identify terminal exons

plotCoverage

Plot read coverage and splice junction read counts

plotFeatures

Plot splice graph and heatmap of expression values

tx

Example transcripts

predictTxFeatures

Splice junction and exon prediction from BAM files

SGFeatureCounts

Constructor function for S4 class SGFeatureCounts

txf_ann

Example transcript features (annotation-based)

predictTxFeaturesPerSample

Identification of splice junctions and exons from BAM file

SGFeatures

Constructor function for S4 class SGFeatures

sgvc_pred

Example splice variant counts (predicted)

si

Example sample information

predictTxFeaturesPerStrand

Identification of splice junctions and exons for a given chromosome and strand

predictVariantEffects

Predict the effect of splice variants on protein-coding transcripts

sgvc_ann_from_bam

Example splice variant counts (annotated) from BAM files

SGVariants

Constructor function for S4 class SGVariants

sgf_pred

Example splice graph features (predicted)

sgfc_ann

Example splice graph feature counts (annotation-based)

sgf_ann

Example splice graph features (annotation-based)

sgfc_pred

Example splice graph feature counts (predicted)

slots

Accessing and replacing metadata columns

splicesiteOverlap

Compatible fragment counts for splice sites

processTerminalExons

Process predicted terminal exons

removeExonsIsolated

Remove exons with no flanking splice junctions

SGSegments

Constructor function for S4 class SGSegments

sgv_ann

Example splice variants (annotation-based)

TxFeatures

Constructor function for S4 class TxFeatures

predictJunctions

Identify splice junctions

sgv_pred

Example splice variants (predicted)

predictSpliced

IRanges-based identification of splice junctions and exons

txf_pred

Example transcript features (predicted)

SGVariantCounts

Constructor function for S4 class SGFeatureCounts

sgvc_ann

Example splice variant counts (annotated)

sgvc_pred_from_bam

Example splice variant counts (predicted) from BAM files

SGSeq (version 1.4.0)

Splice event prediction and quantification from RNA-seq data

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Functions in SGSeq (1.4.0)