Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/calculateFPKM.R

Calculate fragments per kilobase of exon per million reads mapped (FPKM) values from the feature-level counts.

1 | ```
calculateFPKM(x, lengths, ..., subset.row = NULL, subset_row = NULL)
``` |

`x` |
A numeric matrix of counts where features are rows and cells are columns. Alternatively, a SummarizedExperiment or a SingleCellExperiment containing such counts. |

`lengths` |
Numeric vector providing the effective length for each feature in |

`...` |
Further arguments to pass to |

`subset.row` |
A vector specifying the subset of rows of |

`subset_row` |
Soft-deprecated equivalent to the argument above. |

FPKMs are computed by dividing the CPMs by the effective length of each gene in kilobases. For RNA-seq datasets, the effective length is best set to the sum of lengths of all exons; for nucleus sequencing datasets, the effective length may instead be the entire width of the gene body.

A numeric matrix of FPKM values with the same dimensions as `x`

(unless `subset.row`

is specified).

Aaron Lun, based on code by Davis McCarthy

`calculateCPM`

, for the initial calculation of CPM values.

1 2 3 4 | ```
example_sce <- mockSCE()
eff_len <- runif(nrow(example_sce), 500, 2000)
fout <- calculateFPKM(example_sce, eff_len)
str(fout)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.