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 #> <factor> <numeric> <numeric> #> Gene1 Gene1 12.827219643517 916 #> Gene2 Gene2 1.92490265787296 4897 #> Gene3 Gene3 0.048568954144492 2808 #> Gene4 Gene4 0.991640968123529 2910 #> Gene5 Gene5 0.798837709521328 2011 #> Gene6 Gene6 0.507440151502259 8228
# 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) # }