RegspliceResults: RegspliceResults objects.

In regsplice: L1-regularization based methods for detection of differential splicing

Description

RegspliceResults objects contain the results of a regsplice analysis.

Usage

RegspliceResults(gene_IDs)

gene_IDs(x)

## S4 method for signature 'RegspliceResults'
gene_IDs(x)

p_vals(x)

## S4 method for signature 'RegspliceResults'
p_vals(x)

p_adj(x)

## S4 method for signature 'RegspliceResults'
p_adj(x)

LR_stats(x)

## S4 method for signature 'RegspliceResults'
LR_stats(x)

df_tests(x)

## S4 method for signature 'RegspliceResults'
df_tests(x)

Arguments

gene_IDs	Gene identifiers or names (character vector).
x	RegspliceResults object (for accessor functions).

Details

RegspliceResults objects are created with the constructor function RegspliceResults(), which requires the gene IDs as an argument.

Once created, RegspliceResults objects are then populated using the functions fitRegMultiple, fitNullMultiple, fitFullMultiple, and LRTests.

The function summaryTable can be used to display a summary table of the results.

Value

Returns an empty RegspliceResults object.

Fields

gene_IDs

Gene identifiers or names (character vector).

fit_reg_dev

Deviance of fitted regularized (lasso) models from fitRegMultiple.

fit_reg_df

Degrees of freedom of fitted regularized (lasso) models from fitRegMultiple.

fit_null_dev

Deviance of fitted null models from fitNullMultiple.

fit_null_df

Degrees of freedom of fitted null models from fitNullMultiple.

fit_full_dev

Deviance of fitted full models from fitFullMultiple.

fit_full_df

Degrees of freedom of fitted full models from fitFullMultiple.

p_vals

Raw p-values (numeric vector).

p_adj

Multiple testing adjusted p-values (Benjamini-Hochberg false discovery rates, FDR).

LR_stats

Likelihood ratio test statistics.

df_tests

Degrees of freedom of likelihood ratio tests.

Accessor functions

• gene_IDs(): Accesses gene identifiers or names.

• p_vals(): Accesses raw p-values.

• p_adj(): Accesses multiple testing adjusted p-values (Benjamini-Hochberg false discovery rates, FDR).

• LR_stats(): Accesses likelihood ratio test statistics.

• df_tests(): Accesses degrees of freedom of likelihood ratio tests.

See Also

fitRegMultiple fitNullMultiple fitFullMultiple LRTests summaryTable

Examples

# initialize RegspliceResults object
gene_IDs <- paste0("gene", 1:5)
RegspliceResults(gene_IDs)

regsplice documentation built on Nov. 8, 2020, 5:32 p.m.