About tximport

Description

tximport imports transcript-level estimates from various external software and optionally summarizes abundances, counts, and transcript lengths to the gene-level (default) or outputs transcript-level matrices (see txOut argument)

https://rdrr.io/bioc/tximport/man/tximport.html

Supported software (i.e. the type argument):

  • salmon

  • sailfish

  • alevin

  • kallisto

  • rsem

  • stringtie

With type = "none", one can specify the columns containing required information

Scaling

The countsFromAbundance argument has 4 options depedning on whether to generate estimated counts using abundance estimates

  • no - no scaling (default)

  • scaledTPM - scaled up to library size

  • lengthScaledTPM - scaled using the average transcript length over samples and then the library size

  • dtuScaledTPM - scaled using the median transcript length among isoforms of a gene, and then the library size. dtuScaledTPM is designed for differential transcript usage (DTU) analysis in combination with txOut=TRUE, and it requires specifing a tx2gene data.frame

Examples

In /home/USER/SSAPs we execute R

Load a TxDb object and creat the tx2gene data.frame from the TxDb object, this is

Create a named vector files pointing to the quantification files

Import the quantification files using tximport(). By specifying txOut = TRUE, one can obtain transcript-level counts. By default, the function outputs gene-level summarization

If quantification file format is not supported, we can also load the files by specifying required columns (i.e. txIdCol, abundanceCol, countsCol and lengthCol). We using the Salmon quantification files as an exmaple

PreviousBuilding a TxDb objectNextConvert Salmon output to Sleuth-compatible format

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