contribToContigPerFrag: Characterize Individual Contribution Of Single Edges In Tree-Structures

Description

This function helps investigating tree-like structures with the aim of indicating how much individual tree components contribute to compose long stretches.

Usage

contribToContigPerFrag(
  joinMat,
  fullLength = NULL,
  nDig = 3,
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Value

This function returns a matrix of 3 columns for each node identified in rownames of joinMatr for length of longest tree-branches where given edge participates (column sumLen), the (total) number of edges therein (col n.frag) and a relative value (len.rat)

Arguments

joinMat: (matrix) matrix with concatenated edges as rownames (separated by slashes), column sumLen for total length and column n for number of edges
fullLength: (integer) custom total length (useful if the concatenated edges do not cover 100 percent of the original precursor whose fragments are studied)
nDig: (integer) rounding: number of digits for 3rd column len.rat in output
silent: (logical) suppress messages
callFrom: (character) allow easier tracking of messages produced
debug: (logical) additional messages for debugging

Details

contribToContigPerFrag characterizes individual (isolated) contribution of single edges in tree-structures. Typically used to process/exploit summarized trees (as matrix) made by buildTree which makes use of the package data.tree. For example if A,B and C can be joined aa well and B +D, this function will check if A+B+C is longer and if A contributes to the longest tree.

Examples

Run this code

path1 <- matrix(c(17,19,18,17, 4,4,2,3), ncol=2,
  dimnames=list(c("A/B/C/D","A/B/G/D","A/H","A/H/I"),c("sumLen","n")))
contribToContigPerFrag(path1)