Add gene lengths to an SCESet object

addGeneLengths(sce, method = c("generate", "sample"), loc = 7.9,
  scale = 0.7, lengths = NULL)

Arguments

sce

SCESet 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

SCESet with added gene lengths

Details

This function adds simulated gene lengths to the fData slot of an SCESet object that can be used for calculating length normalised expression values such as TPM or FPKM. The generate simulates lengths using a (rounded) log-normal distribution, with the default loc and scale parameters based on human 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 SCESet...
sce <- addGeneLengths(sce) head(fData(sce))
#> Gene GeneMean Length #> Gene1 Gene1 1.885070e+00 2874 #> Gene2 Gene2 5.651522e+00 1169 #> Gene3 Gene3 1.109488e+01 2330 #> Gene4 Gene4 8.549893e-03 4415 #> Gene5 Gene5 5.620109e-04 7288 #> Gene6 Gene6 4.884267e-02 4316
# 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) # }