Add gene lengths

Add gene lengths to an SingleCellExperiment object

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.

Value

SingleCellExperiment with added gene lengths

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.

Examples

# Default generate method
sce <- simpleSimulate()
#> Simulating means...
#> Simulating counts...
#> Creating final dataset...
sce <- addGeneLengths(sce)
head(rowData(sce))
#> DataFrame with 6 rows and 3 columns
#>              Gene   GeneMean    Length
#>       <character>  <numeric> <numeric>
#> Gene1       Gene1 0.39274964      4891
#> Gene2       Gene2 2.48067014      2804
#> Gene3       Gene3 1.96955391      1325
#> Gene4       Gene4 0.00337284      2314
#> Gene5       Gene5 1.01863282      6135
#> Gene6       Gene6 0.05567822      9756
# Sample method (human coding genes)
if (FALSE) {
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)
}