detectLoop {TreeSummarizedExperiment} | R Documentation |
detectLoop
detects loopsDetect loops
detectLoop
detects loops
detectLoop(tax_tab)
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. |
a data frame
Ruizhu Huang
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)