Compare pseudoaligned counts to aligned counts.

Compare pseudoaligned counts to aligned counts.

plotPseudoVsAlignedCounts(object, ...)

# S4 method for bcbioRNASeq
plotPseudoVsAlignedCounts(object, genes = NULL,
  title = "Pseudoaligned vs. aligned counts", ...)

Arguments

object	Object.
...	Passthrough to acidplots::plotCountsCorrelationHeatmap() when genes = NULL or acidplots::plotCountsCorrelation() when genes are defined.
genes	character. Gene identifiers.
title	character(1). Title.

Note

Currently supported for salmon or kallisto. The function will intentionally error for datasets containing aligned counts in the primary counts assay.

Updated 2019-09-16.

Examples

data(bcb)

## Correlation heatmap.
plotPseudoVsAlignedCounts(bcb)
#> Making the rownames and colnames human readable.
#> Returning with the sample names unmodified.
#> Censoring 29 genes containing an NA value.

## Individual genes.
## Checking the most expressed aligned genes here.
aligned <- assay(bcb, i = "aligned")
genes <- rowSums(aligned) %>% sort %>% tail(n = 2L) %>% names()
plotPseudoVsAlignedCounts(bcb, genes = genes)
#> Making the rownames and colnames human readable.
#> Returning with the sample names unmodified.