getRpkm: Get measurements from rawData

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

Get measurements from rawData

Description

Gets the rpkm, tpm, signal or cpm measurement from SummarizedExperiment or SingleCellExperiment object.

Usage

  getRpkm(rawData)
  getTpm(rawData)
  getSignal(rawData)
  getCpm(rawData)

Arguments

rawData

SummarizedExperiment or SingleCellExperiment object.

Value

Returns the matrix of rpkm, tpm, signal or cpm measurement.

Author(s)

Ge Tan

References

https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/

Examples

  ## Not run: 
    ## bulk
    file <- "/srv/gstore/projects/p1688/CountQC_20201_2017-08-15--20-52-44/input_dataset.tsv"
    param <- ezParam(list(dataRoot="/srv/gstore/projects",
                          refBuild="Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-05-31"))
    input <- EzDataset$new(file=file, dataRoot=param$dataRoot)
    rawData <- loadCountDataset(input, param)
    getRpkm(rawData)
    getTpm(rawData)
    getSignal(rawData)
    getCpm(rawData)
    
    ## single cell
    param <- ezParam(list(dataRoot="/srv/gstore/projects",
                          refBuild="Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26",
                          scProtocol="smart-Seq2"
                          ))
    input = list()
    input[['Name']] = 'NCC_Trpv5_Tomato_sc_A01'
    input[['Species']] = ''
    input[['refBuild']] = 'Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26'
    input[['paired']] = 'false'
    input[['featureLevel']] = 'gene'
    input[['refFeatureFile']] = 'genes.gtf'
    input[['transcriptTypes']] = 'protein_coding,rRNA,tRNA,Mt_rRNA,Mt_tRNA'
    input[['ResultDir']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01'
    input[['CellDataset']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01-dataset.tsv'
    input[['CountMatrix']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01-counts.mtx'
    input[['CountMatrixColNames']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01-counts.colNames'
    input[['CountMatrixRowNames']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01-counts.rowNames'
    input[['Stats']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01-stats.txt'
    input[['CellCyclePhase']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01-CellCyclePhase.txt'
    input[['BAM']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01.bam'
    input[['BAI']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01.bam.bai'
    input[['PreprocessingLog']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01_preprocessing.log'
    input[['STARLog']] = 'p2838/SCCountsApp_28469_2018-12-05--15-25-05/NCC_Trpv5_Tomato_sc_A01/NCC_Trpv5_Tomato_sc_A01_STAR.log'
    input <- EzDataset$new(meta=input, dataRoot=param$dataRoot)
    rawData <- loadSCCountDataset(input, param)
    getTpm(rawData)
    getRpkm(rawData)
    getCpm(rawData)
  
## End(Not run)

uzh/ezRun documentation built on April 29, 2024, 10:31 a.m.