calculate_bayes_factors_2dkcde: calculate_bayes_factors_2dkcde

In alextkalinka/delboy: Differential-representation analysis by Elastic-net Logistic regression with BinOmial-thinning validitY tests

Description

Calculates log Bayes Factors using a 2d kernel cumulative distribution estimate for True and False Positives along the dimensions of log fold change (LFC) and expression level (EL): Pr(LFC, EL | TP)/Pr(LFC, EL | FP)).

Usage

calculate_bayes_factors_2dkcde(
  data,
  data_bs,
  fc_column,
  expr_column,
  group_column
)

Arguments

data	A data frame containing data for which Bayes Factors will be calculated.
data_bs	A data frame containing bootstrap-sampled data for which a 2D kernel cumulative distribution estimate will be calculated for the data points in data.
fc_column	A character string naming the log fold change column.
expr_column	A character string naming the expression level column.
group_column	A character string naming the grouping column containing only True_Positive and False_Positive entries.

Value

A list containing the following elements:

• kcde_TP - an object of class kcde for True_Positives.

• kcde_FP - an object of class kcde for False_Positives.

• cum_prob_BF - a data frame containing cumulative probability estimates and Bayes Factors for the data in data.

alextkalinka/delboy documentation built on Feb. 2, 2022, 4:19 p.m.