surf-class: SURF class

In fchen365/surf: Statistical Utility for RBP (RNA binding protein) Functions

Description

The surf class is an all-in-one analytic object used in SURF framework. A surf object contains results of DrSeq (analysis module 1), FASeq (analysis module 2), and DASeq (discovery module 1). In addition, it also contain gene (isoform) parts list, parsing from genome annotation. The gene parts list is essential for ATR event construction. If the any analysis module or discovery module is performed, the sample metadata will also be recorded. Each of the components mentioned above can be accessed through a function listed below.

Usage

## S4 method for signature 'surf'
genePartsList(object)

## S4 method for signature 'surf'
drseqResults(object)

## S4 method for signature 'surf'
faseqResults(object)

## S4 method for signature 'surf'
daseqResults(object)

Arguments

object

a surf object output by daseq.

Value

a surf object.

References

Chen, F., & Keles, S. (2020). SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins. Genome Biology, 21(1), 1-23.

See Also

genePartsList, drseqResults, faseqResults, daseqResults, sampleData.

fchen365/surf documentation built on June 18, 2021, 12:02 p.m.