summaries {mia} | R Documentation |
To query a SummarizedExperiment
for interesting features, several
functions are available.
getTopTaxa( x, top = 5L, method = c("mean", "sum", "median"), abund_values = "counts" ) ## S4 method for signature 'SummarizedExperiment' getTopTaxa( x, top = 5L, method = c("mean", "sum", "median", "prevalence"), abund_values = "counts" ) getUniqueTaxa(x, ...) ## S4 method for signature 'SummarizedExperiment' getUniqueTaxa(x, rank = NULL) countDominantTaxa(x, group = NULL, ...) ## S4 method for signature 'SummarizedExperiment' countDominantTaxa(x, group = NULL, ...) ## S4 method for signature 'SummarizedExperiment' summary(object, abund_values = "counts")
x |
A
|
top |
Numeric value, how many top taxa to return. Default return top five taxa. |
method |
Specify the method to determine top taxa. Either sum, mean, median or prevalence. Default is 'mean'. |
abund_values |
a |
... |
Additional arguments passed on to |
rank |
A single character defining a taxonomic rank. Must be a value of
the output of |
group |
With group, it is possible to group the observations in an
overview. Must be one of the column names of |
object |
A
|
The getTopTaxa
extracts the most top
abundant “FeatureID”s
in a SummarizedExperiment
object.
The getUniqueTaxa
is a basic function to access different taxa at a
particular taxonomic rank.
countDominantTaxa
returns information about most dominant
taxa in a tibble. Information includes their absolute and relative
abundances in whole data set.
The summary
will return a summary of counts for all samples and
features in
SummarizedExperiment
object.
The getTopTaxa
returns a vector of the most top
abundant
“FeatureID”s
The getUniqueTaxa
returns a vector of unique taxa present at a
particular rank
The countDominantTaxa
returns an overview in a tibble. It contains dominant taxa
in a column named *name*
and its abundance in the data set.
The summary
returns a list with two tibble
s
Leo Lahti, Tuomas Borman and Sudarshan A. Shetty
perCellQCMetrics
,
perFeatureQCMetrics
,
addPerCellQC
,
addPerFeatureQC
,
quickPerCellQC
data(GlobalPatterns) top_taxa <- getTopTaxa(GlobalPatterns, method = "mean", top = 5, abund_values = "counts") top_taxa # Gets the overview of dominant taxa dominant_taxa <- countDominantTaxa(GlobalPatterns, rank = "Genus") dominant_taxa # With group, it is possible to group observations based on specified groups # Gets the overview of dominant taxa dominant_taxa <- countDominantTaxa(GlobalPatterns, rank = "Genus", group = "SampleType", na.rm= TRUE) dominant_taxa # Get an overview of sample and taxa counts summary(GlobalPatterns) # Get unique taxa at a particular taxonomic rank getUniqueTaxa(GlobalPatterns, "Phylum")