Slot aligned counts

Slot aligned counts

Usage

slotAlignedCounts(object, ...)

# S4 method for bcbioRNASeq
slotAlignedCounts(object)

Arguments

object

Object.

...

Additional arguments.

Value

Modified object.

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.

Note

Updated 2020-12-22.

Author

Michael Steinbaugh

Examples

## bcbioRNASeq ====
uploadDir <- system.file("extdata/bcbio", package = "bcbioRNASeq")
## Fast mode skips import of aligned counts.
bcb <- bcbioRNASeq(uploadDir, fast = TRUE)
#> 
#> ────────────────────────────────────────────────────────────────────────────────
#> bcbioRNASeq
#> ────────────────────────────────────────────────────────────────────────────────
#> ℹ Importing bcbio-nextgen RNA-seq run.
#> ── Run info
#> uploadDir:
#> /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp7t0ccV/temp_libpathb0f511e0f2fd/bcbioRNASeq/extdata/bcbio
#> projectDir: 2018-03-18_GSE65267-merged
#> ℹ 6 samples detected:
#> • control_rep1
#> • control_rep2
#> • control_rep3
#> • fa_day7_rep1
#> • fa_day7_rep2
#> • fa_day7_rep3
#> → Importing /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp7t0ccV/temp_libpathb0f511e0f2fd/bcbioRNASeq/extdata/bcbio/2018-03-18_GSE65267-merged/project-summary.yaml using yaml::`read_yaml()`.
#> ! Data versions are missing.
#> → Importing /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp7t0ccV/temp_libpathb0f511e0f2fd/bcbioRNASeq/extdata/bcbio/2018-03-18_GSE65267-merged/programs.txt using base::`read.table()`.
#> → Importing /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp7t0ccV/temp_libpathb0f511e0f2fd/bcbioRNASeq/extdata/bcbio/2018-03-18_GSE65267-merged/bcbio-nextgen.log using base::`readLines()`.
#> ! bcbio-nextgen.log file is empty.
#> → Importing /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp7t0ccV/temp_libpathb0f511e0f2fd/bcbioRNASeq/extdata/bcbio/2018-03-18_GSE65267-merged/bcbio-nextgen-commands.log using base::`readLines()`.
#> ! bcbio-nextgen-commands.log file is empty.
#> ── Sample metadata
#> → Getting sample metadata from YAML.
#> → Getting sample quality control metrics from YAML.
#> ── Counts
#> ─── tximport
#> → Importing /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp7t0ccV/temp_libpathb0f511e0f2fd/bcbioRNASeq/extdata/bcbio/2018-03-18_GSE65267-merged/tx2gene.csv using base::`read.table()`.
#> ! No transcript versions to modify.
#> → Importing salmon transcript-level counts from quant.sf files using tximport 1.30.0.
#> countsFromAbundance: lengthScaledTPM
#> txOut: FALSE
#> reading in files with read_tsv
#> 1 
#> 2 
#> 3 
#> 4 
#> 5 
#> 6 
#> 
#> summarizing abundance
#> summarizing counts
#> summarizing length
#> ── Feature metadata
#> bcbio GTF file:
#> /n/app/bcbio/dev/genomes/Mmusculus/GRCm38_90/rnaseq/ref-transcripts.gtf
#> ! bcbio GTF file is not accessible.
#> ! Slotting empty ranges into `rowRanges()`.
#> ── Metadata
#> ✔ bcbio RNA-seq run imported successfully.
"aligned" %in% SummarizedExperiment::assayNames(bcb)
#> [1] FALSE
bcb <- slotAlignedCounts(bcb)
#> → Importing aligned counts from featureCounts.
#> → Importing /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp7t0ccV/temp_libpathb0f511e0f2fd/bcbioRNASeq/extdata/bcbio/2018-03-18_GSE65267-merged/combined.counts using base::`read.table()`.
"aligned" %in% SummarizedExperiment::assayNames(bcb)
#> [1] TRUE