Package index • tximeta

Package overview

tximeta-package: Import transcript quantification with metadata

Main import functions

tximeta(): Import transcript quantification with metadata

summarizeToGene(<SummarizedExperiment>): Summarize estimated quantitites to gene-level

linkedTxome: linking data to metadata

makeLinkedTxome() loadLinkedTxome(): Make and load linked transcriptomes (linked GTF and FASTA)

makeLinkedTxpData(): Make linked transcript data (linked GRanges)

Mixed reference transcripts

importData(): Import quantification across mixed reference transcripts

inspectDigests(): Inspect digest matches from importData() imported data

updateMetadata(): Update transcript metadatda for importData() imported data

Add information to object

addCDS(): Add CDS to rowRanges of a transcript-level SummarizedExperiment

addExons(): Add exons to rowRanges of a transcript-level SummarizedExperiment

addIds(): Add IDs to rowRanges of a SummarizedExperiment

Retrieve information from object

retrieveCDNA(): Retrieve the cDNA transcript sequence for a SummarizedExperiment

retrieveDb(): Retrieve the TxDb or EnsDb associated with a SummarizedExperiment

Other helpers

splitSE(): Split SummarizedExperiment by gene categories

makeDGEList(): Make a DGEList from tximeta output

getTximetaBFC() setTximetaBFC(): Get or set the directory of the BiocFileCache used by tximeta