isContaminant {mia} | R Documentation |
The decontam
functions isContaminant
and
isNotContaminant
are made available for
SummarizedExperiment
objects.
## S4 method for signature 'SummarizedExperiment' isContaminant( seqtab, abund_values = "counts", name = "isContaminant", concentration = NULL, control = NULL, batch = NULL, threshold = 0.1, normalize = TRUE, detailed = TRUE, ... ) ## S4 method for signature 'SummarizedExperiment' isNotContaminant( seqtab, abund_values = "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", ...)
seqtab, x |
|
abund_values |
A single character value for selecting the
|
name |
A name for the column of the colData in which the contaminant information should be stored. |
concentration |
|
control |
|
batch |
|
threshold |
numeric scalar. See
|
normalize, detailed |
logical scalar. See
|
... |
|
for isContaminant
/ isNotContaminant
a DataFrame
or for addContaminantQC
/addNotContaminantQC
a modified object
of class(x)
decontam:isContaminant
,
decontam:isNotContaminant
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)