detectLoop: Detect loops 'detectLoop' detects loops

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

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) 

TreeSummarizedExperiment documentation built on Dec. 8, 2020, 2 a.m.