getDominant | R Documentation |
These functions return information about the most dominant taxa in a
SummarizedExperiment
object.
getDominant(
x,
assay.type = assay_name,
assay_name = "counts",
rank = NULL,
other.name = "Other",
n = NULL,
complete = TRUE,
...
)
## S4 method for signature 'SummarizedExperiment'
getDominant(
x,
assay.type = assay_name,
assay_name = "counts",
rank = NULL,
other.name = "Other",
n = NULL,
complete = TRUE,
...
)
addDominant(x, name = "dominant_taxa", other.name = "Other", n = NULL, ...)
## S4 method for signature 'SummarizedExperiment'
addDominant(
x,
name = "dominant_taxa",
other.name = "Other",
n = NULL,
complete = FALSE,
...
)
x |
|
assay.type |
|
assay_name |
Deprecated. Use |
rank |
|
other.name |
|
n |
|
complete |
|
... |
Additional arguments passed on to |
name |
|
addDominant
extracts the most abundant taxa in a
SummarizedExperiment
object, and stores the information in the colData
. It is a wrapper for
getDominant
.
With rank
parameter, it is possible to agglomerate taxa based on
taxonomic ranks. E.g. if 'Genus' rank is used, all abundances of same Genus
are added together, and those families are returned.
See agglomerateByRank()
for additional arguments to deal with
missing values or special characters.
If the rank
is not specifying a taxonomy rank from
taxonomyRanks(x)
, the function
agglomerates rows with agglomerateByVariable()
.
getDominant
returns a named character vector x
while addDominant
returns
SummarizedExperiment
with additional column in colData
named *name*
.
data(GlobalPatterns)
x <- GlobalPatterns
# Finds the dominant taxa.
sim.dom <- getDominant(x, rank="Genus")
# Add information to colData
x <- addDominant(x, rank = "Genus", name="dominant_genera")
colData(x)
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