isContaminant: decontam functions

In FelixErnst/mia: Microbiome analysis

decontam functions

Description

The decontam functions isContaminant and isNotContaminant are made available for SummarizedExperiment objects.

Usage

addContaminantQC(x, name = "isContaminant", ...)

addNotContaminantQC(x, name = "isNotContaminant", ...)

## S4 method for signature 'SummarizedExperiment'
isContaminant(
  seqtab,
  assay.type = assay_name,
  assay_name = "counts",
  concentration = NULL,
  control = NULL,
  batch = NULL,
  threshold = 0.1,
  normalize = TRUE,
  detailed = TRUE,
  ...
)

## S4 method for signature 'SummarizedExperiment'
isNotContaminant(
  seqtab,
  assay.type = assay_name,
  assay_name = "counts",
  control = NULL,
  threshold = 0.5,
  normalize = TRUE,
  detailed = TRUE,
  ...
)

## S4 method for signature 'SummarizedExperiment'
addContaminantQC(x, name = "contaminant", ...)

## S4 method for signature 'SummarizedExperiment'
addNotContaminantQC(x, name = "not_contaminant", ...)

Arguments

name	Character scalar. A name for the column of the colData where results will be stored. (Default: "contaminant" or "not_contaminant")
...	for isContaminant/ isNotContaminant: arguments passed on to decontam:isContaminant or decontam:isNotContaminant for addContaminantQC/addNotContaminantQC: arguments passed on to isContaminant/ isNotContaminant
seqtab, x	a SummarizedExperiment
assay.type	Character scalar. Specifies the name of assay used in calculation. (Default: "counts")
assay_name	Deprecated. Use assay.type instead.
concentration	Character scalar or NULL. Defining a column with numeric values from the colData to use as concentration information. (Default: NULL)
control	Character scalar or NULL. Defining a column with logical values from the colData to define control and non-control samples. (Default: NULL)
batch	Character scalar or NULL. Defining a column with values interpretable as a factor from the colData to use as batch information. (Default: NULL)
threshold	Numeric scalar.. See decontam:isContaminant or decontam:isNotContaminant
normalize	Logical scalar. See decontam:isContaminant or decontam:isNotContaminant
detailed	Logical scalar. If TRUE, the return value is a data.frame containing diagnostic information on the contaminant decision. If FALSE, the return value is a logical vector containing the binary contaminant classifications. (Default: TRUE)

Value

for isContaminant/ isNotContaminant a DataFrame or for addContaminantQC/addNotContaminantQC a modified object of class(x)

See Also

decontam:isContaminant, decontam:isNotContaminant

Examples

data(esophagus)
# setup of some mock data just for example
colData(esophagus)$concentration <- c(1, 2, 3)
colData(esophagus)$control <- c(FALSE, FALSE, TRUE)

isContaminant(
    esophagus,
    method = "frequency",
    concentration = "concentration"
    )
esophagus <- addContaminantQC(
    esophagus,
    method = "frequency",
    concentration = "concentration"
    )
rowData(esophagus)

isNotContaminant(esophagus, control = "control")
esophagus <- addNotContaminantQC(esophagus, control = "control")
rowData(esophagus)

FelixErnst/mia documentation built on April 3, 2025, 2:15 p.m.