resolveLoop: Resolve loops 'resolveLoop' resolve loops by adding suffix to...

In fionarhuang/TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

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)

fionarhuang/TreeSummarizedExperiment documentation built on June 11, 2025, 9:42 a.m.