addGeneLengths {splatter} | R Documentation

## 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)

[Package splatter version 1.14.1 Index]