resolveLoop {TreeSummarizedExperiment} | R Documentation

## Resolve loops `resolveLoop` resolve loops by adding suffix to the child node. The suffix is "_i" where 'i' is a number. Please see examples.

### Description

Resolve loops `resolveLoop` resolve loops by adding suffix to the child node. The suffix is "_i" where 'i' is a number. Please see examples.

### Usage

    resolveLoop(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

    # example 1
    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)
    resolveLoop(tax_tab = df)

    # example 2
    taxTab <- data.frame(R1 = rep("A", 5),
                         R2 = c("B1", rep("B2", 3), ""),
                         R3 = c("C1", "C2", "C3", "", ""),
                         R4 = c("D1", "D2", "D3", "", ""),
                         R5 = paste0("E", 1:5))

    resolveLoop(tax_tab = taxTab)
    # example 3
    taxTab <- data.frame(R1 = rep("A", 6),
                         R2 = c("B1", rep("B2", 4), ""),
                         R3 = c("C1", "C2", "C3", "", "", ""),
                         R4 = c("D1", "D2", "D3", "", "", ""),
                         R5 = paste0("E", 1:6))

    resolveLoop(tax_tab = taxTab)

     # example 3
    taxTab <- data.frame(
                R1 = rep("A", 5),
                R2 = c("B1", rep("B2", 3), "B3"),
                R3 = c("C1", "C2", "C3", NA, NA),
                R4 = c("D1", "D2", "D3", NA, NA),
                R5 = paste0("E", 1:5))
    resolveLoop(tax_tab = taxTab)

[Package TreeSummarizedExperiment version 2.2.0 Index]