loadSCCountDataset: Loads the count dataset of single cell experiment

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

Loads the count dataset of single cell experiment

Description

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

Usage

  loadSCCountDataset(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.

Details

A SingleCellExperiment object with

• assays: counts, presentFlag, RPKM, TPM

• rowData: seqAnno

• colData: cell dataset

• metadata: isLog, featureLevel, type, param

Author(s)

Ge Tan

References

https://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html#create-instances-of-singlecellexperiment

See Also

loadCountDataset

Examples

  ## Not run: 
    ## smart-Seq2 platform
    library(ezRun)
    param = list()
    param[['cores']] = '1'
    param[['ram']] = '2'
    param[['scratch']] = '10'
    param[['node']] = ''
    param[['process_mode']] = 'DATASET'
    param[['name']] = 'SCCount_QC'
    param[['refBuild']] = 'Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_89-2017-05-31'
    param[['refFeatureFile']] = 'genes.gtf'
    param[['featureLevel']] = 'gene'
    param[['mail']] = '[e-mail]'
    param[['dataRoot']] = '/srv/gstore/projects'
    param[['resultDir']] = 'p2497/p2497-SCCountQC'
    output = list()
    output[['Name']] = 'SCCount_QC'
    output[['Species']] = ''
    output[['refBuild']] = 'Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_89-2017-05-31'
    output[['Static Report [Link]']] = 'p2497/p2497-SCCountQC/SCCount_QC/00index.html'
    output[['Report [File]']] = 'p2497/p2497-SCCountQC/SCCount_QC'
    input = '/srv/gstore/projects/p2497/SCCountsApp_23745_2018-01-05--11-55-48/dataset.tsv'
    
    input = EzDataset$new(file=input, dataRoot=param$dataRoot)
    param <- ezParam(param)
    output = EzDataset$new(meta=output, dataRoot=param$dataRoot)
    
    sce <- loadSCCountDataset(input, param)
    
    ## 10x
    library(ezRun)
    param = list()
    param[['cores']] = '8'
    param[['ram']] = '100'
    param[['scratch']] = '200'
    param[['node']] = ''
    param[['process_mode']] = 'SAMPLE'
    param[['samples']] = 'AVM_sample_26092018,Sample_28092018'
    param[['name']] = 'SCCount_QC'
    param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26'
    param[['paired']] = 'false'
    param[['strandMode']] = 'both'
    param[['refFeatureFile']] = 'genes.gtf'
    param[['featureLevel']] = 'gene'
    param[['transcriptTypes']] = ''
    param[['minReadsPerCell']] = '1'
    param[['minReadsPerGene']] = '1'
    param[['minGenesPerCell']] = '1'
    param[['specialOptions']] = ''
    param[['mail']] = '[e-mail]'
    param[['dataRoot']] = '/srv/gstore/projects'
    param[['resultDir']] = 'p2284/SCCountQC_30486_2018-11-07--14-32-21'
    output = list()
    output[['Name']] = 'Sample_28092018'
    output[['Species']] = 'Homo sapiens (human)'
    output[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26'
    output[['refFeatureFile']] = 'genes.gtf'
    output[['Static Report [Link]']] = 'p2284/SCCountQC_30486_2018-11-07--14-32-21/Sample_28092018_SCCountQC/00index.html'
    output[['seuratOnline [Link]']] = 'http://fgcz-shiny.uzh.ch/fgcz_seuratOnline_app/?data=p2284/SCCountQC_30486_2018-11-07--14-32-21/Sample_28092018_SCCountQC/sce.rds'
    output[['Report [File]']] = 'p2284/SCCountQC_30486_2018-11-07--14-32-21/Sample_28092018_SCCountQC'
    input = list()
    input[['Name']] = 'Sample_28092018'
    input[['ResultDir']] = 'p2284/CellRangerCount_30477_NOV28_o4866_2018-10-11--09-10-56/Sample_28092018'
    input[['Report']] = 'p2284/CellRangerCount_30477_NOV28_o4866_2018-10-11--09-10-56/Sample_28092018/outs/web_summary.html'
    input[['BAM']] = 'p2284/CellRangerCount_30477_NOV28_o4866_2018-10-11--09-10-56/Sample_28092018/outs/possorted_genome_bam.bam'
    input[['BAI']] = 'p2284/CellRangerCount_30477_NOV28_o4866_2018-10-11--09-10-56/Sample_28092018/outs/possorted_genome_bam.bam.bai'
    input[['Species']] = 'Homo sapiens (human)'
    input[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26'
    input[['refFeatureFile']] = 'genes.gtf'
    input[['featureLevel']] = 'gene'
    input[['CountMatrix']] = 'p2284/CellRangerCount_30477_NOV28_o4866_2018-10-11--09-10-56/Sample_28092018/outs/filtered_gene_bc_matrices'
    input[['Sample Id']] = 'bfs_185587'
    input[['Order Id']] = '4866'
    input = EzDataset$new(meta=input, dataRoot=param$dataRoot)
    param <- ezParam(param)
    param$scProtocol <- "10x"
    output = EzDataset$new(meta=output, dataRoot=param$dataRoot)
        
    sce <- loadSCCountDataset(input, param)
  
## End(Not run)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.