infoCand: Get information of candidates

In fionarhuang/treeclimbR: An algorithm to find optimal signal levels in a tree

Get information of candidates

Description

Extract information about candidates.

Usage

infoCand(object)

Arguments

object

An output object from evalCand.

Value

A data.frame with information about candidates.

Author(s)

Ruizhu Huang

Examples

suppressPackageStartupMessages({
    library(TreeSummarizedExperiment)
    library(ggtree)
})

## Simulate some data
data(tinyTree)
ggtree(tinyTree, branch.length = "none") +
   geom_text2(aes(label = node)) +
   geom_hilight(node = 13, fill = "blue", alpha = 0.3) +
   geom_hilight(node = 18, fill = "orange", alpha = 0.3)
set.seed(1)
pv <- runif(19, 0, 1)
pv[c(seq_len(5), 13, 14, 18)] <- runif(8, 0, 0.001)

fc <- sample(c(-1, 1), 19, replace = TRUE)
fc[c(seq_len(3), 13, 14)] <- 1
fc[c(4, 5, 18)] <- -1
df <- data.frame(node = seq_len(19),
                 pvalue = pv,
                 logFoldChange = fc)

## Get candidates
ll <- getCand(tree = tinyTree, score_data = df,
               node_column = "node",
               p_column = "pvalue",
               sign_column = "logFoldChange")

## Evaluate candidates
cc <- evalCand(tree = tinyTree, levels = ll$candidate_list,
               score_data = df, node_column = "node",
               p_column = "pvalue", sign_column = "logFoldChange",
               limit_rej = 0.05)

## Get summary info about candidates
out <- infoCand(object = cc)
out

fionarhuang/treeclimbR documentation built on May 19, 2024, 1:18 p.m.