RunMiQC: Run miQC on a Seurat object

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Run miQC on a Seurat object

Description

Run miQC on a Seurat object

Usage

RunMiQC(
  object,
  percent.mt = "percent.mt",
  nFeature_RNA = "nFeature_RNA",
  posterior.cutoff = 0.75,
  model.type = "linear",
  model.slot = "flexmix_model",
  verbose = TRUE,
  backup.option = "percentile",
  backup.percentile = 0.99,
  backup.percent = 5,
  ...
)

Arguments

object	Seurat object
percent.mt	(character) Name of the column in the Seurat metadata that contains the percent of reads attributed to mitochondrial genes. Defaults to "percent.mt".
nFeature_RNA	(character) Name of the column in the Seurat metadata that contains the number of reads per cell. Defaults to "nFeature_RNA".
posterior.cutoff	numeric) The posterior probability of a cell being part of the compromised distribution, a number between 0 and 1. Any cells below the appointed cutoff will be marked to keep. Defaults to 0.75.
model.type	(character) What type of model to generate. A linear mixture model ("linear") is recommended, but currently b-spline ("spline") and two-degree polynomial ("polynomial") are also supported Default = "linear".
verbose	Boolean. TRUE to show progress messages, FALSE to hide progress messages
backup.option	(character) In case flexmix fails to build a 2 cluster mixture model, what should RunMiQC do: "percent" (set miQC.keep values according to backup.percent), "percentile" (set miQC.keep values according to backup.percentile), "pass" (return original Seurat object), or "halt" (stop RunMiQC). "percent", "percentile", and "pass" are useful when processing multiple Seurat objects sequentially.
backup.percentile	(numeric) What percentile to use as cutoff in case flexmix fails to build a 2 cluster mixture model. Will only be used if backup.option is "percentile".
backup.percent	(numeric) What percent to use as cutoff in case flexmix fails to build a 2 cluster mixture model. Will only be used if backup.option is "percent".

Details

(Copied verbatim from miQC) _Function to fit a two-distribution mixture model on a Seurat object and find those cells probabistically determined to be compromised by the mixture model._

Value

Returns a Seurat object with probabilities and "keep" decisions stored as "miQC.probability" and "miQC.keep" in the object metadata, respectively.

References

Hippen et al. (2021) miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. bioRxiv doi: 10.1101/2021.03.03.433798

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.