getPhi: Calculate a global phi for all cell types

In huangyh09/DCATS: Differential Composition Analysis Transformed by a Similarity matrix

Calculate a global phi for all cell types

Description

Assuming all cell types share the same phi. This global phi can be calculate by pooling all cell types together to fit a beta binomial distribution.

Usage

getPhi(count_mat, design_mat)

Arguments

count_mat	A matrix of composition sizes (n_sample, n_cluster) for each cluster in each sample
design_mat	A matrix of testing candidate factors (n_sample, n_factor) with same sample order as count_mat

Value

A number indicating a global phi for all cell types

Examples

K <- 3
totals1 = c(100, 800, 1300, 600)
totals2 = c(250, 700, 1100)
diri_s1 = rep(1, K) * 20
diri_s2 = rep(1, K) * 20
simil_mat = DCATS::create_simMat(K, confuse_rate=0.2)
sim_dat <- DCATS::simulator_base(totals1, totals2, diri_s1, diri_s2, simil_mat)
sim_count = rbind(sim_dat$numb_cond1, sim_dat$numb_cond2)
sim_design = data.frame(condition = c("g1", "g1", "g1", "g1", "g2", "g2", "g2"))
phi = DCATS::getPhi(sim_count, sim_design)

huangyh09/DCATS documentation built on Nov. 25, 2022, 7:02 a.m.