counts: Count Matrix Accessors

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

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

Usage

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

Arguments

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.

Value

matrix.

Author(s)

Michael Steinbaugh, Lorena Pantano

See Also

• tpm().

• tmm().

• DESeq2::counts().

• DESeq2::rlog().

• DESeq2::varianceStabilizingTransformation().

Other Data Functions: metrics, tmm, tpm

Examples

# 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()

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.