SpectrumScore-class: An S4 class to represent a scored spectrum

In transite: RNA-binding protein motif analysis

Description

An S4 class to represent a scored spectrum

Getter Method get_adj_r_squared

Getter Method get_model_degree

Getter Method get_model_residuals

Getter Method get_model_slope

Getter Method get_model_f_statistic

Getter Method get_model_f_statistic_p_value

Getter Method get_consistency_score

Getter Method get_consistency_score_p_value

Getter Method get_consistency_score_n

Usage

get_adj_r_squared(object)

## S4 method for signature 'SpectrumScore'
get_adj_r_squared(object)

get_model_degree(object)

## S4 method for signature 'SpectrumScore'
get_model_degree(object)

get_model_residuals(object)

## S4 method for signature 'SpectrumScore'
get_model_residuals(object)

get_model_slope(object)

## S4 method for signature 'SpectrumScore'
get_model_slope(object)

get_model_f_statistic(object)

## S4 method for signature 'SpectrumScore'
get_model_f_statistic(object)

get_model_f_statistic_p_value(object)

## S4 method for signature 'SpectrumScore'
get_model_f_statistic_p_value(object)

get_consistency_score(object)

## S4 method for signature 'SpectrumScore'
get_consistency_score(object)

get_consistency_score_p_value(object)

## S4 method for signature 'SpectrumScore'
get_consistency_score_p_value(object)

get_consistency_score_n(object)

## S4 method for signature 'SpectrumScore'
get_consistency_score_n(object)

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

## S4 method for signature 'SpectrumScore,ANY'
plot(x)

Arguments

object	SpectrumScore object
x	SpectrumScore object

Value

Object of type SpectrumScore

Slots

adj_r_squared

adjusted R^2 of polynomial model

degree

degree of polynomial (integer between 0 and 5)

residuals

residuals of the polynomial model

slope

coefficient of the linear term of the polynomial model (spectrum "direction")

f_statistic

F statistic from the F test used to determine the degree of the polynomial model

f_statistic_p_value

p-value associated with the F statistic

consistency_score

raw local consistency score of the spectrum

consistency_score_p_value

p-value associated with the local consistency score

consistency_score_n

number of permutations performed to calculate p-value of local consistency score (permutations performed before early stopping criterion reached)

plot

spectrum plot

Examples

new("SpectrumScore",
    adj_r_squared = 0,
    degree = 0L,
    residuals = 0,
    slope = 0,
    f_statistic = 0,
    f_statistic_p_value = 1,
    consistency_score = 1,
    consistency_score_p_value = 1,
    consistency_score_n = 1000L,
    plot = NULL
)

transite documentation built on Nov. 8, 2020, 5:27 p.m.