BANDITS_data-class: BANDITS_data class

In SimoneTiberi/BANDITS: BANDITS: Bayesian ANalysis of DIfferenTial Splicing

BANDITS_data class

Description

BANDITS_data contains all the information required to perform differential transcript usage (DTU). BANDITS_data associates each gene (genes), to its transcript ids (transcripts), effective transcript lengths (effLen), equivalence classes (classes) and respective counts (counts). The same structure is also used for groups of genes with reads/fragments compatible with >1 gene (with uniqueId == FALSE); in this case the 'genes' field contains all the genes ids in the group. Created via create_data.

Usage

## S4 method for signature 'BANDITS_data'
show(object)

Arguments

object

a 'BANDITS_data' object.

Value

• show(object): returns the number of genes and transcripts in the BANDITS_data object.

Slots

genes

list of gene names: each element is a vector of 1 or more gene names indicating the genes to be analyzed together.

transcripts

list of transcript names: each element is a vector of 1 or more transcript names indicating the transcripts matching the gene names in the corresponding element of @genes object.

effLen

list of transcript effective lengths: each element is a vector of 1 or more numbers, indicating the effective length of the transcripts in the corresponding element of @transcripts object.

classes

list of matrices: the (i,j) element of each matrix is 1 if the i-th transcript is present in the j-th equivalence class, 0 otherwise.

counts

list of matrices: the (i,j) element indicates the reads/fragments compatible with the i-th equivalence class in sample j.

uniqueId

logical, it indicates if the element contains one gene to be analyzed alone (TRUE), or more genes to be analyzed jointly (FALSE).

all_genes

vector, it lists all the genes to be analyzed (with at least 2 transcripts).

Author(s)

Simone Tiberi [e-mail]

See Also

create_data, filter_transcripts, eff_len_compute

Examples

# load the pre-computed data:
data("input_data", package = "BANDITS")
show(input_data)

SimoneTiberi/BANDITS documentation built on Nov. 15, 2023, 2:35 p.m.