Extracting values of useful attributes of SummarizedExperiment objects

Description

Several functions are provided that can extract various attribnutes from an object of class SummarizedExperiment generated by IntEREst functions, e.g. interest(), interest, and readInterestResults. It is possible to extract sample annotations using getAnnotation function. One can also extract the scaled retention levels of the introns/exons using scaledRetention() function. Notes that colData and rowData methods of SummarizedExperiment class can also be used to extract row and column data.

Usage

getAnnotation(x)
scaledRetention(x)

Arguments

Value

Various data types (data.frame/vector) dependent on the function used. See the "Description" for more information.

Author(s)

Ali Oghabian

See Also

SummarizedExperiment-class addAnnotation counts-method plot-method

Examples

# Retrieve the sample annotations from mdsChr22Obj
getAnnotation(mdsChr22Obj)
# Retrieving the scaled retention levels from mdsChr22Obj
head(scaledRetention(mdsChr22Obj))

#for row and column data SummarizedExperiment methods can be used
head(rowData(mdsChr22Obj))
colData(mdsChr22Obj)