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Import and summarize transcript-level estimates for transcript- and gene-level analysis

Description of methods and analysis described in:

• Charlotte Soneson, Michael I. Love, Mark D. Robinson.Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences,F1000Research, 4:1521, December 2015. doi: 10.12688/f1000research.7563.1

Imports transcript-level abundance, estimated counts andtranscript lengths, and summarizes into matrices for use with downstreamstatistical analysis packages such as edgeR, DESeq2, limma-voom.Average transcript length, weighted bysample-specific transcript abundance estimates, is provided as a matrixwhich can be used as an offset for different expression ofgene-level counts.

See examples in thevignette.

Notes:

• tximport as of version 1.3.9 will import inferential replicates(Gibbs samples or bootstrap samples) from Salmon, Sailfish or kallisto.
• Though we provide here functionality for performing gene-leveldifferential expression using summarized transcript-level estimates,this is does not mean we suggest that usersonly perform gene-levelanalysis. Gene-level differential expression can be complementedwith transcript- or exon-level analysis. The argumenttxOut=TRUEcan be used to generate transcript-level matrices.