getAbundance {mia} | R Documentation |
These are functions for extracting abundances present in assay(x)
.
These functions are convenience wrapper around subsetting columns or rows
from assay(x,name)
.
getAbundanceSample(x, sample_id, abund_values = "counts") ## S4 method for signature 'SummarizedExperiment' getAbundanceSample(x, sample_id = NULL, abund_values = "counts") getAbundanceFeature(x, feature_id, abund_values) ## S4 method for signature 'SummarizedExperiment' getAbundanceFeature(x, feature_id = NULL, abund_values = "counts")
x |
A
|
sample_id |
A “SampleID” from which user wants to extract the
abundances of “FeatureID”. This is essentially a column name in
|
abund_values |
a |
feature_id |
A “FeatureID” for which user wants to extract the
abundances from all of “SampleID” in
|
getAbundanceSample
returns abundance values for all
“FeatureIDs” in a user specified “SampleID”.
getAbundanceFeature
returns abundance values in all “SampleIDs”
for user specified “FeatureID”.
getAbundanceSample
and getAbundanceFeature
return a
numeric matrix of the abundance values for all
“SampleIDs”/“FeatureIDs”
Sudarshan A. Shetty
# getAbundanceSample data(GlobalPatterns) getAbundanceSample(GlobalPatterns, sample_id = 'CC1', abund_values = 'counts') # getAbundanceFeature getAbundanceFeature(GlobalPatterns, feature_id = '522457', abund_values = 'counts')