wrMisc (version 2.0.0)

countSameStartEnd: Count Same Start- And End- Sites Of Edges (Or Fragments)

Description

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.

Usage

countSameStartEnd(
  frag,
  minFreq = 2,
  nDig = 4,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

frag

(matrix) 1st column beg start-sites, 2nd column end end-sites of edges, rownames to precise fragment identities are recommended

minFreq

(integer) min number of accumulated sites for taking into account (allows filtering with large datasets)

nDig

(integer) rounding: number of digits for columns beg.rat and end.rat in output

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allows easier tracking of messages produced#' @return This function returns a matrix of 6 columns: input (beg and end), beg.n, beg.rat, end.n, end.rat

See Also

to build initial tree buildTree, contribToContigPerFrag, simpleFragFig

Examples

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)