counts: Count Matrix Accessors
In WeiSong-bio/roryk-bcbioRNASeq: RNA-Seq Utilities

Description Usage Arguments Value Author(s) See Also Examples

By default, counts() returns the raw counts. Normalized counts, including transcripts per million (TPM) can be accessed using the "normalized" argument.

1 2	## S4 method for signature 'bcbioRNASeq' counts(object, normalized = FALSE)

object

Object.

normalized

Logical or character indicating which normalization method to apply:

FALSE: Raw counts (tximport).
TRUE: DESeq2 normalized counts. Calculated on the fly.
"tpm": Transcripts per million (tximport).
"tmm": edgeR trimmed mean of M-values. Calculated on the fly.
"rlog": DESeq2 log2 regularized log transformation.
"vst": DESeq2 log2 variance stabilizing transformation.
"rle": Relative log expression transformation.

matrix.

Michael Steinbaugh, Lorena Pantano

tpm().
tmm().
DESeq2::counts().
DESeq2::rlog().
DESeq2::varianceStabilizingTransformation().

Other Data Functions: metrics, tmm, tpm

# bcbioRNASeq ====
counts(bcb_small, normalized = FALSE) %>% summary()
counts(bcb_small, normalized = TRUE) %>% summary()
counts(bcb_small, normalized = "tpm") %>% summary()
counts(bcb_small, normalized = "tmm") %>% summary()
counts(bcb_small, normalized = "rle") %>% summary()

# log2 scale
counts(bcb_small, normalized = "rlog") %>% summary()
counts(bcb_small, normalized = "vst") %>% summary()