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.
contribToContigPerFrag(joinMat, fullLength = NULL, nDig = 3)
(matrix) matrix with concatenated edges as rownames (separated by slashes), column
(integer) custom total length (useful if the concatenated edges do not cover 100 percent of the original precursor whose fragments are studied)
(integer) rounding: number of digits for 3rd column
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 (
to build tree
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.