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> #> 1 Gene1 0.0370520 3077 #> 2 Gene2 5.1457391 1099 #> 3 Gene3 0.2357753 811 #> 4 Gene4 0.4452486 3692 #> 5 Gene5 0.1680624 3066 #> 6 Gene6 0.9869200 1228
# 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) # }