contribToContigPerFrag {wrMisc} | R 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 |
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 |
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)