View source: R/countSameStartEnd.R
countSameStartEnd | R Documentation |
Suppose a parent sequence/string 'ABCDE' gets cut in various fragments (eg 'ABC','AB' ...).
countSameStartEnd
counts how many (ie re-occuring) start- and end- sites of edges do occur in the input-data.
The input is presented as matrix of/indicating start- and end-sites of edges.
The function is used to characterize partially redundant edges and accumulation of cutting/breakage sites.
countSameStartEnd(frag, minFreq = 2, nDig = 4)
frag |
(matrix) 1st column |
minFreq |
(integer) min number of accumulated sites for taking into account (allows filtering with large datasets) |
nDig |
(integer) rounding: number of digits for columns |
matrix of 6 columns: input (beg and end), beg.n, beg.rat, end.n, end.rat
to build initial tree buildTree
, contribToContigPerFrag
, simpleFragFig
frag1 <- cbind(beg=c(2,3,7,13,13,15,7,9,7, 3,3,5), end=c(6,12,8,18,20,20,19,12,12, 4,5,7))
rownames(frag1) <- letters[1:nrow(frag1)]
countSameStartEnd(frag1)
simpleFragFig(frag1)
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