detectLoop {TreeSummarizedExperiment} | R Documentation

## Detect loops `detectLoop` detects loops

### Description

Detect loops `detectLoop` detects loops

### Usage

    detectLoop(tax_tab)

### Arguments

`tax_tab` | a data frame where columns store hierarchical levels. The columns from the left to the right correspond nodes from the root to the leaf.

### Value

a data frame

### Author(s)

Ruizhu Huang

### Examples

    df <- data.frame(A = rep("a", 8),
                     B = rep (c("b1", "b2", "b3", "b4"), each = 2),
                     C = paste0("c", c(1, 2, 2, 3:7)),
                     D = paste0("d", 1:8))

    # The result means that a loop is caused by 'b1' and 'b2' in column 'B' and
    # 'c2' in column 'C' (a-b1-c2; a-b2-c2)
    detectLoop(tax_tab = df)

    df <- data.frame(R1 = rep("A", 6),
                         R2 = c("B1", rep("B2", 4), "B3"),
                         R3 = c("C1", "C2", "C3", NA, NA, NA),
                         R4 = c("D1", "D2", "D3", NA, NA, NA),
                         R5 = paste0("E", 1:6))
    detectLoop(tax_tab = df)

    df <- data.frame(R1 = rep("A", 7),
                         R2 = c("B1", rep("B2", 4), "B3", "B3"),
                         R3 = c("C1", "C2", "C3", "", "", "", ""),
                         R4 = c("D1", "D2", "D3", "", "", "", ""),
                         R5 = paste0("E", 1:7))
    detectLoop(tax_tab = df)

    df <- data.frame(R1 = rep("A", 7),
                         R2 = c("B1", rep("B2", 4), "B3", "B3"),
                         R3 = c("C1", "C2", "C3", NA, NA, NA, NA),
                         R4 = c("D1", "D2", "D3", NA, NA, NA, NA),
                         R5 = paste0("E", 1:7))
    detectLoop(tax_tab = df)

[Package TreeSummarizedExperiment version 2.2.0 Index]