tpm.on.subset {DGEobj.utils} | R Documentation |
Calculate TPM for a subsetted DGEobj
Description
Calculates TPM for a heavily subsetted DGEobj. The function will calculate TPM using the original data but returns a DGEobj with the subset.
Usage
tpm.on.subset(dgeObj, applyFilter = TRUE)
Arguments
dgeObj |
A DGEobj data structure |
applyFilter |
Default = TRUE. If TRUE, reduces to the filtered gene list. FALSE returns all genes in the raw data. |
Details
TPM should be calculated on a full dataset with only low signal genes removed. tpm.on.subset therefore allows calculation of TPM after heavy filtering of a DGEobj.
Internally, convertCounts uses edgeR's fpkm() to calculate FPKM and converts to TPM using the formula provided by [Harold Pimental](https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/).
Value
A matrix of TPM values
Examples
## Not run:
# NOTE: Requires the edgeR package
dgeObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
tpm <- tpm.on.subset(dgeObj)
## End(Not run)
[Package DGEobj.utils version 1.0.6 Index]