CCDF: Function to compute (un)conditional cumulative distribution...
In ccdf: Distribution-Free Single-Cell Differential Expression Analysis

Description Usage Arguments Value Examples

View source: R/CCDF.R

Function to compute (un)conditional cumulative distribution function (CDF), used by plot_CCDF function.

CCDF(
  Y,
  X,
  Z = NULL,
  method = c("linear regression", "logistic regression", "RF"),
  fast = TRUE,
  space_y = FALSE,
  number_y = length(Y)
)

`Y`	a numeric vector of size `n` containing the preprocessed expressions from `n` samples (or cells).
`X`	a data frame containing numeric or factor vector(s) of size `n` containing the variable(s) to be tested (the condition(s) to be tested).
`Z`	a data frame containing numeric or factor vector(s) of size `n` containing the covariate(s).
`method`	a character string indicating which method to use to compute the CCDF, either `'linear regression'`, `'logistic regression'` and `'permutations'` or `'RF'` for Random Forests. Default is `'linear regression'` since it is the method used in the test.
`fast`	a logical flag indicating whether the fast implementation of logistic regression should be used. Only if `'dist_permutations'` is specified. Default is `TRUE`.
`space_y`	a logical flag indicating whether the y thresholds are spaced. When `space_y` is `TRUE`, a regular sequence between the minimum and the maximum of the observations is used. Default is `FALSE`.
`number_y`	an integer value indicating the number of y thresholds (and therefore the number of regressions) to perform the test. Default is `length(Y)`.

A list with the following elements:

cdf: a vector of the cumulative distribution function of a given gene.
ccdf: a vector of the conditional cumulative distribution function of a given gene, computed given X. Only if Z is NULL.
ccdf_nox: a vector of the conditional cumulative distribution function of a given gene, computed given Z only (i.e. X is ignored.). Only if Z is not NULL.
ccdf_x: a vector of the conditional cumulative distribution function of a given gene, computed given X and Z. Only if Z is not NULL.
y_sort: a vector of the sorted expression points at which the CDF and the CCDFs are calculated.
x_sort: a vector of the variables associated with y_sort.
z_sort: a vector of the covariates associated with y_sort. Only if Z is not NULL.

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X <- as.factor(rbinom(n=100, size = 1, prob = 0.5))
Y <- ((X==1)*rnorm(n = 50,0,1)) + ((X==0)*rnorm(n = 50,0.5,1))
res <- CCDF(Y,data.frame(X=X),method="linear regression")