ASpediaFI-class: ASpediaFI class

Description Usage Arguments Value Slots Accessors Examples

Description

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

Usage

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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

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

nachoryu/ASpediaFI documentation built on April 6, 2020, 10:49 a.m.