ASpediaFI-class {ASpediaFI} | R Documentation

## ASpediaFI class

### Description

ASpediaFI class is a wrapper of ASpediaFI functionalities and a container of inputs and outputs.

### Usage

    ASpediaFI(sample.names, bam.files, conditions)

### Arguments

`sample.names` | a character vector of sample names (or IDs)
`bam.files` | a character vector of paths to RNA-Seq BAM files
`conditions` | a vector of sample conditions (e.g. mutation status)

### Value

ASpediaFI object

### Slots

  `samples`: a data frame containing information about samples. The first three columns should be names, BAM file paths, and conditions.

  `events`: a list of AS events extracted from a GTF file.

  `gtf`: a `GRanges` object containing genomic features extracted from a GTF file.

  `psi`: a `SummarizedExperiment` object containing AS event quantification

  `network`: an `igraph` object containing a query-specific subnetwork as a result of DRaWR.

  `gene.table, as.table, pathway.table`: data frames containing gene nodes, AS event nodes, and pathway nodes.

### Accessors

In the following, 'x' represents a `ASpediaFI` object:

  `samples(x), samples(x) <- value`: get or set sample information. value must be a data frame containing sample information.

  `events(x), events(x) <- value`: get or set AS event annotations. value must be a list of annotations.

  `gtf(x), gtf(x) <- value`: get or set a `GRanges` object containing GTF. value must be a `GRanges` object.

  `psi(x), psi(x) <- value`: get or set PSI values. value must be a `SummarizedExperiment` object.

  `network(x), network(x) <- value`: get or set final subnetwork. value must be an `igraph` object.

  `gene.table(x), gene.table(x) <- value`: get or set gene node tables. value must be a data frame containing information about gene nodes.

  `as.table(x), as.table(x) <- value`: get or set AS node tables. value must be a data frame containing information about AS nodes.

  `pathway.table(x), pathway.table(x) <- value`: get or set pathway node tables. value must be a data frame containing information about pathway nodes.

### Examples

    bamWT <- system.file('extdata/GSM3167290.subset.bam', package = 'ASpediaFI')
    GSE114922.ASpediaFI <- ASpediaFI(
        sample.names = 'GSM3167290',
        bam.files = bamWT, conditions = 'WT'
    )

[Package ASpediaFI version 1.1.4 Index]