Seurat: PercentageFeatureSet – R documentation

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PercentageFeatureSet

Calculate the percentage of all counts that belong to a given set of features

Description

This function enables you to easily calculate the percentage of all the counts belonging to a subset of the possible features for each cell. This is useful when trying to compute the percentage of transcripts that map to mitochondrial genes for example. The calculation here is simply the column sum of the matrix present in the counts slot for features belonging to the set divided by the column sum for all features times 100.

Usage

PercentageFeatureSet(
  object,
  pattern = NULL,
  features = NULL,
  col.name = NULL,
  assay = NULL
)

Arguments

`object`	A Seurat object
`pattern`	A regex pattern to match features against
`features`	A defined feature set. If features provided, will ignore the pattern matching
`col.name`	Name in meta.data column to assign. If this is not null, returns a Seurat object with the proportion of the feature set stored in metadata.
`assay`	Assay to use

Value

Returns a vector with the proportion of the feature set or if md.name is set, returns a Seurat object with the proportion of the feature set stored in metadata.

Examples

data("pbmc_small")
# Calculate the proportion of transcripts mapping to mitochondrial genes
# NOTE: The pattern provided works for human gene names. You may need to adjust depending on your
# system of interest
pbmc_small[["percent.mt"]] <- PercentageFeatureSet(object = pbmc_small, pattern = "^MT-")

Seurat

Tools for Single Cell Genomics

v4.0.1

GPL-3 | file LICENSE

Authors

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17