contribToContigPerFrag: Characterize individual contribution of single edges in...

View source: R/contribToContigPerFrag.R

contribToContigPerFragR Documentation

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. 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.

Usage

contribToContigPerFrag(joinMat, fullLength = NULL, nDig = 3)

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

Value

matrix of 3 columns: with 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)

See Also

to build tree buildTree

Examples

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)

wrMisc documentation built on Jan. 7, 2023, 1:27 a.m.