bcbioRNASeq Additional Run Data Accessor

This method is used to access alternative count matrices with differing dimensions from the primary counts stored as a SummarizedExperiment.

# S4 method for bcbioRNASeq
bcbio(object, type)

# S4 method for bcbioRNASeq
bcbio(object, type) <- value

# S4 method for bcbioRNADataSet
bcbio(object, type)

# S4 method for bcbioRNADataSet
bcbio(object, type) <- value

Arguments

object

Object.
type

Type of data to retrieve.
value

Value to assign.

Value

slot object.

Details

Additional count matrices of interest include:

  • Aligned counts generated by STAR and featureCounts.

  • Transcript-level gene expression, for sleuth analysis.

  • miRNA expression counts.

Since these matrices don't necessarily contain the same number of columns and rows as the counts imported with tximport(), it is preferable to store this information as alternative callers.

Note

By default, we store the quasi-aligned (a.k.a. lightweight) gene expression counts generated by salmon into in a SummarizedExperiment::SummarizedExperiment using tximport(). These counts should be accessed using the counts() generic. Any additional transformations of those original counts, including tpm(), rlog(), or tmm() are stored alongside the raw counts.

Examples

# tximport list
txi <- bcbio(bcb, "tximport")
class(txi)
#> [1] "list"
length(txi)
#> [1] 4
names(txi)
#> [1] "abundance"           "counts"              "length"             
#> [4] "countsFromAbundance"

# featureCounts matrix
fc <- bcbio(bcb, "featureCounts")
class(fc)
#> [1] "matrix"
dim(fc)
#> [1] 999   4
colnames(fc)
#> [1] "group1_1" "group1_2" "group2_1" "group2_2"