bcbioRNASeq

S4 class containing RNA-seq counts and metadata generated by bcbio.

Details

bcbioRNASeq is a subclass of SummarizedExperiment designed to store an RNA-seq analysis. This class contains raw read counts and transcripts per million (TPM) generated by tximport().

The metadata accessor contains:

  • Sample summary statistics (a.k.a. metrics).

  • Ensembl annotations.

  • Server run paths.

  • R local environment information, including sessionInfo().

Slots

bcbio

SimpleList containing additional bcbio run data with dimensions that don't match the count matrix. This is currently used to store STAR featureCounts aligned counts.

See also

Examples

uploadDir <- system.file("extdata/bcbio", package = "bcbioRNASeq")
bcb <- loadRNASeq(uploadDir)
#> 2017-05-23_rnaseq
#> 4 samples detected
#> Reading project-summary.yaml
#> Genome: Mus musculus (mm10)
#> Loading Ensembl annotations from AnnotationHub
#> 2017-10-27
#> EnsDB AH57770: Mus musculus Ensembl 90
#> Parsed with column specification:
#> cols(
#>   enstxp = col_character(),
#>   ensgene = col_character()
#> )
#> Reading bcbio run information
#> Parsed with column specification:
#> cols(
#>   genome = col_character(),
#>   resource = col_character(),
#>   version = col_datetime(format = "")
#> )
#> Warning: bcbio-nextgen.log missing
#> Warning: bcbio-nextgen-commands.log missing
#> Reading salmon counts using tximport
#> 1 
#> Parsed with column specification:
#> cols(
#>   Name = col_character(),
#>   Length = col_integer(),
#>   EffectiveLength = col_double(),
#>   TPM = col_double(),
#>   NumReads = col_double()
#> )
#> 2 
#> Parsed with column specification:
#> cols(
#>   Name = col_character(),
#>   Length = col_integer(),
#>   EffectiveLength = col_double(),
#>   TPM = col_double(),
#>   NumReads = col_double()
#> )
#> 3 
#> Parsed with column specification:
#> cols(
#>   Name = col_character(),
#>   Length = col_integer(),
#>   EffectiveLength = col_double(),
#>   TPM = col_double(),
#>   NumReads = col_double()
#> )
#> 4 
#> Parsed with column specification:
#> cols(
#>   Name = col_character(),
#>   Length = col_integer(),
#>   EffectiveLength = col_double(),
#>   TPM = col_double(),
#>   NumReads = col_double()
#> )
#> 
#> summarizing abundance
#> summarizing counts
#> summarizing length
#> Generating internal DESeqDataSet for quality control
#> using just counts from tximport
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> Performing rlog transformation
#> Performing variance stabilizing transformation
#> Reading STAR featureCounts aligned counts
#> Parsed with column specification:
#> cols(
#>   .default = col_integer(),
#>   id = col_character()
#> )
#> See spec(...) for full column specifications.
#> Warning: Unannotated genes detected in counts matrix (0.594%)