getTPM {recount} | R Documentation

## Compute a TPM matrix based on a RangedSummarizedExperiment object

### Description

For some analyses you might be interested in transforming the counts into TPMs which you can do with this function. This function uses the gene-level RPKMs to derive TPM values (see Details).

### Usage

    getTPM(rse, length_var = "bp_length", mapped_var = NULL)

### Arguments

`rse` | A RangedSummarizedExperiment-class object as downloaded with download_study.
`length_var` | A length 1 character vector with the column name from `rowData(rse)` that has the coding length. For gene level objects from recount this is `bp_length`. If `NULL`, then it will use `width(rowRanges(rse))` which should be used for exon RSEs.
`mapped_var` | A length 1 character vector with the column name from `colData(rse)` that has the number of reads mapped. For recount RSE object this would be `mapped_read_count`. If `NULL` (default) then it will use the column sums of the counts matrix. The results are different because not all mapped reads are mapped to exonic segments of the genome.

### Details

For gene RSE objects, you will want to specify the `length_var` because otherwise you will be adjusting for the total gene length instead of the total exonic sequence length of the gene.

As noted in https://support.bioconductor.org/p/124265/, Sonali Arora et al computed TPMs in https://www.biorxiv.org/content/10.1101/445601v2 using the formula: TPM = FPKM / (sum of FPKM over all genes/transcripts) * 10^6

Arora et al mention in their code that the formula comes from https://doi.org/10.1093/bioinformatics/btp692; specifically `1.1.1 Comparison to RPKM estimation` where they mention an important assumption: Under the assumption of uniformly distributed reads, we note that RPKM measures are estimates of ...

There's also a blog post by Harold Pimentel explaining the relationship between FPKM and TPM: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/.

### Value

A matrix with the TPM values.

### Author(s)

Sonali Arora, Leonardo Collado-Torres

### References

https://www.biorxiv.org/content/10.1101/445601v2 https://arxiv.org/abs/1104.3889

### See Also

getRPKM

### Examples

    ## Compute the TPM matrix from the raw gene-level base-pair counts.
    tpm <- getTPM(rse_gene_SRP009615)

[Package recount version 1.13.1 Index]