isContaminant: decontam functions

In microbiome/mia: Microbiome analysis

decontam functions

Description

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

Usage

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

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

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

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

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

Arguments

seqtab, x	a SummarizedExperiment
assay.type	A single character value for selecting the assay to use.
assay_name	a single character value for specifying which assay to use for calculation. (Please use assay.type instead. At some point assay_name will be disabled.)
name	A name for the column of the colData in which the contaminant information should be stored.
concentration	NULL or a single character value. Defining a column with numeric values from the colData to use as concentration information. (default: concentration = NULL)
control	NULL or a single character value. Defining a column with logical values from the colData to define control and non-control samples. (default: control = NULL)
batch	NULL or a single character value. Defining a column with values interpretable as a factor from the colData to use as batch information. (default: batch = NULL)
threshold	numeric scalar. See decontam:isContaminant or decontam:isNotContaminant
normalize, detailed	logical scalar. See decontam:isContaminant or decontam:isNotContaminant
...	for isContaminant/ isNotContaminant: arguments passed on to decontam:isContaminant or decontam:isNotContaminant for addContaminantQC/addNotContaminantQC: arguments passed on to isContaminant/ isNotContaminant

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
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")
colData(esophagus)

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

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.