calculateTPM: Calculate TPMs

In scuttle: Single-Cell RNA-Seq Analysis Utilities

Description

Calculate transcripts-per-million (TPM) values for expression from feature-level counts.

Usage

calculateTPM(x, ...)

## S4 method for signature 'ANY'
calculateTPM(x, lengths = NULL, ...)

## S4 method for signature 'SummarizedExperiment'
calculateTPM(x, ..., assay.type = "counts", exprs_values = NULL)

## S4 method for signature 'SingleCellExperiment'
calculateTPM(x, lengths = NULL, size.factors = NULL, ...)

Arguments

x	A numeric matrix of counts where features are rows and cells are columns. Alternatively, a SummarizedExperiment or a SingleCellExperiment containing such counts.
...	For the generic, arguments to pass to specific methods. For the ANY method, further arguments to pass to calculateCPM. For the SummarizedExperiment method, further arguments to pass to the ANY method. For the SingleCellExperiment method, further arguments to pass to the SummarizedExperiment method.
lengths	Numeric vector providing the effective length for each feature in x. Alternatively NULL, see Details.
assay.type	A string specifying the assay of x containing the count matrix.
exprs_values	Soft-deprecated equivalents to the arguments above.
size.factors	A numeric vector containing size factors to adjust the library sizes. If NULL, the library sizes are used directly.

Details

For read count data, this function assumes uniform coverage along the (effective) length of the transcript. Thus, the number of transcripts for a gene is proportional to the read count divided by the transcript length. Here, the division is done before calculation of the library size to compute per-million values, where calculateFPKM will only divide by the length after library size normalization.

For UMI count data, this function should be run with lengths=NULL, i.e., no division by the effective length. This is because the number of UMIs is a direct (albeit biased) estimate of the number of transcripts.

Value

A numeric matrix of TPM values with the same dimensions as x (unless subset.row is specified).

Author(s)

Aaron Lun, based on code by Davis McCarthy

See Also

calculateCPM, on which this function is based.

Examples

example_sce <- mockSCE()
eff_len <- runif(nrow(example_sce), 500, 2000)
tout <- calculateTPM(example_sce, lengths = eff_len)
str(tout)

scuttle documentation built on Dec. 19, 2020, 2 a.m.