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 0.001748482 1527 #> 2 Gene2 0.040891176 4195 #> 3 Gene3 0.027987949 15546 #> 4 Gene4 1.004302577 5228 #> 5 Gene5 2.437182383 1591 #> 6 Gene6 0.794571297 2089
# 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) # }