slotAlignedCounts: Slot aligned counts

In hbc/bcbioRnaseq: Bcbio RNA-Seq

Slot aligned counts

Description

Slot aligned counts

Usage

slotAlignedCounts(object, ...)

## S4 method for signature 'bcbioRNASeq'
slotAlignedCounts(object)

Arguments

object	Object.
...	Additional arguments.

Details

This function loads aligned counts (e.g. STAR, HISAT2) from the bcbio final output directory into the bcbioRNASeq object, so we can visually inspect correlations with the primary pseudoaligned counts.

Value

Modified object.

Note

Updated 2020-12-22.

Author(s)

Michael Steinbaugh

Examples

## bcbioRNASeq ====
uploadDir <- system.file("extdata/bcbio", package = "bcbioRNASeq")
## Fast mode skips import of aligned counts.
bcb <- bcbioRNASeq(uploadDir, fast = TRUE)
"aligned" %in% SummarizedExperiment::assayNames(bcb)
bcb <- slotAlignedCounts(bcb)
"aligned" %in% SummarizedExperiment::assayNames(bcb)

hbc/bcbioRnaseq documentation built on Sept. 15, 2024, 9:10 a.m.