loadCountDataset: Loads the count dataset

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Loads the count dataset

Description

Loads the count dataset with the given input and param into a SummarizedExperiment object.

Usage

  loadCountDataset(input, param)

Arguments

input

A EzDataset object with ‘dataRoot’ and filepath of ‘input_dataset.tsv’.

param

A list of parameters: dataRoot the root directory of the files. expressionName if specified, this will be used as the column name... knownExpressionNames ...or otherwise known expression names that occur in the dataset will be used. ezRef@refBuild if specified, the sequence annotation will be extracted from ezFeatureAnnotation(). transcriptTypes if specified, only the defined transcript type will be used. sigThresh the threshold... useSigThresh ...and whether it should be used. featureLevel if equal to "gene" and the feature level of the dataset to "isoform", the rawdata will be passed to aggregateCountsByGene() before returning it.

Value

A SummarizedExperiment object with

• assays: counts, presentFlag, RPKM, TPM, (signal)

• rowData: seqAnno

• colData: input$meta

• metadata: isLog, featureLevel, type, countName, param

Author(s)

Ge Tan

References

https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

See Also

loadSCCountDataset

Examples

  ## Not run: 
    ## gene-level counts; gene-level return
    file <- "/srv/gstore/projects/p2828/CountQC_28750_2018-08-13--15-38-33/input_dataset.tsv"
    param <- ezParam(list(dataRoot="/srv/gstore/projects",
                          refBuild="Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26"))
    input <- EzDataset$new(file=file, dataRoot=param$dataRoot)
    rawData <- loadCountDataset(input, param)
    
    ## isoform-level counts; gene-level return
    file <- "/srv/gstore/projects/p2828/CountQC_29754_2018-09-24--15-15-29/input_dataset.tsv"
    param <- ezParam(list(dataRoot="/srv/gstore/projects",
                          refBuild="Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26",
                          featureLevel="gene",
                          expressionName=""))
    input <- EzDataset$new(file=file, dataRoot=param$dataRoot)
    rawData <- loadCountDataset(input, param)
    
    ## isoform-level counts; isoform-level return
    file <- "/srv/gstore/projects/p2828/CountQC_29754_2018-09-24--15-15-29/input_dataset.tsv"
    param <- ezParam(list(dataRoot="/srv/gstore/projects",
                          refBuild="Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26",
                          featureLevel="isoform",
                          expressionName=""))
    input <- EzDataset$new(file=file, dataRoot=param$dataRoot)
    rawData <- loadCountDataset(input, param)
  
## End(Not run)

uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.