ASpediaFI-class | R Documentation |
ASpediaFI class is a wrapper of ASpediaFI functionalities and a container of inputs and outputs.
ASpediaFI(sample.names, bam.files, conditions)
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) |
ASpediaFI object
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.
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.
bamWT <- system.file('extdata/GSM3167290.subset.bam', package = 'ASpediaFI') GSE114922.ASpediaFI <- ASpediaFI( sample.names = 'GSM3167290', bam.files = bamWT, conditions = 'WT' )
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