dmDSdata-class: dmDSdata object

Description

dmDSdata contains expression, in counts, of genomic features such as exons or transcripts and sample information needed for the differential splicing (DS) analysis. It can be created with function dmDSdata.

Usage

dm_counts(x, ...)
"dm_counts"(x)
dm_samples(x, ...)
"dm_samples"(x)
"counts"(object)
samples(x, ...)
"samples"(x)
"names"(x)
"length"(x)
"["(x, i, j)

Arguments

...

Other parameters that can be defined by methods using this generic.

object, x

dmDSdata object.

i, j

Parameters used for subsetting.

Value

counts(object): Get a data frame with counts.
samples(x): Get a data frame with the sample information.
names(x): Get the gene names.
length(x): Get the number of genes.
x[i, j]: Get a subset of dmDSdata object that consists of counts for genes i and samples j.
dm_counts(object): Get the counts slot.
dm_samples(object): Get the samples slot.

Slots

counts: MatrixList of expression, in counts, of genomic features. Rows correspond to genomic features, such as exons or transcripts. Columns correspond to samples. MatrixList is partitioned in a way that each of the matrices in a list contains counts for a single gene.
samples: Data frame with information about samples. It must contain variables: sample_id of unique sample names and group which groups samples into conditions.

Examples

Run this code

###################################
### Differential splicing analysis
###################################

d <- data_dmDSdata

head(counts(d))
samples(d)
head(names(d))
length(d)
d[1:20, ]
d[1:20, 1:3]