addGeneLengths: Add gene lengths

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

Add gene lengths

Description

Add gene lengths to an SingleCellExperiment object

Usage

addGeneLengths(
  sce,
  method = c("generate", "sample"),
  loc = 7.9,
  scale = 0.7,
  lengths = NULL
)

Arguments

sce	SingleCellExperiment to add gene lengths to.
method	Method to use for creating lengths.
loc	Location parameter for the generate method.
scale	Scale parameter for the generate method.
lengths	Vector of lengths for the sample method.

Details

This function adds simulated gene lengths to the rowData slot of a SingleCellExperiment object that can be used for calculating length normalised expression values such as TPM or FPKM. The generate method simulates lengths using a (rounded) log-normal distribution, with the default loc and scale parameters based on human protein-coding genes. Alternatively the sample method can be used which randomly samples lengths (with replacement) from a supplied vector.

Value

SingleCellExperiment with added gene lengths

Examples

# Default generate method
sce <- simpleSimulate()
sce <- addGeneLengths(sce)
head(rowData(sce))
# Sample method (human coding genes)
## Not run: 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(GenomicFeatures)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
tx.lens <- transcriptLengths(txdb, with.cds_len = TRUE)
tx.lens <- tx.lens[tx.lens$cds_len > 0, ]
gene.lens <- max(splitAsList(tx.lens$tx_len, tx.lens$gene_id))
sce <- addGeneLengths(sce, method = "sample", lengths = gene.lens)

## End(Not run)

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.