counts: Counts

In hbc/bcbioRNASeq: Bcbio RNA-Seq

Counts

Description

Counts

Usage

counts(object, ...)
counts(object, ...) <- value

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

Arguments

object	Object.
normalized	character(1) or logical(1). Normalization method to apply: FALSE: Raw counts. When using a tximport-compatible caller, these are length scaled by default (see countsFromAbundance argument). When using a featureCounts-compatible caller, these are integer. tximport caller-specific normalizations: "tpm": Transcripts per million. Additional gene-level-specific normalizations: TRUE / "sf": Size factor (i.e. library size) normalized counts. See DESeq2::sizeFactors for details. "fpkm": Fragments per kilobase per million mapped fragments. Requires fast = FALSE in bcbioRNASeq() call and gene annotations in rowRanges() with defined width(). See DESeq2::fpkm() for details. "vst": Variance-stabilizing transformation (log2). Requires fast = FALSE to be set during bcbioRNASeq() call. See DESeq2::varianceStabilizingTransformation() for more information. "tmm": Trimmed mean of M-values. Calculated on the fly. See edgeR::calcNormFactors() for details. "rle": Relative log expression transformation. Calculated on the fly. See relativeLogExpression() for details. "rlog": Deprecated. Regularized log transformation (log2). No longer calculated automatically during bcbioRNASeq() call, but may be defined in legacy objects. See DESeq2::rlog() for details. Note that VST is more performant and now recommended by default instead. Note that logical(1) support only applies to counts(). Other functions in the package require character(1) and use match.arg() internally.
...	Additional arguments.
value	Value to assign.

Details

By default, return the raw counts. Normalized counts in a variety of formats can be accessed using the normalized argument.

Value

matrix.

Note

Updated 2022-03-07.

Author(s)

Michael Steinbaugh, Lorena Pantano

References

• TMM: Robinson and Oshlack (2010).

• RLE: Anders and Huber (2010).

See Also

• tximport::tximport().

• DESeq2::counts().

• DESeq2::sizeFactors().

• DESeq2::varianceStabilizingTransformation().

• DESeq2::rlog().

• DESeq2::fpkm().

• edgeR::calcNormFactors().

• tmm().

• relativeLogExpression().

Examples

## bcbioRNASeq ====
data(bcb)
summary(counts(bcb))

hbc/bcbioRNASeq documentation built on Sept. 17, 2024, 5:47 a.m.