addGeneLengths {splatter} | R Documentation |
Add gene lengths to an SingleCellExperiment object
addGeneLengths(sce, method = c("generate", "sample"), loc = 7.9, scale = 0.7, lengths = NULL)
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. |
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.
SingleCellExperiment with added gene lengths
# Default generate method sce <- simpleSimulate() sce <- addGeneLengths(sce) head(rowData(sce)) # 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) ## End(Not run)