wrMisc (version 1.2.3)

buildTree: Connect edges to form tree and extract all possible branches

Description

It is assumed that multiple fragments from a common ancestor bay be charcterized by the their start- and end-sites by integer values. For example, If 'abcdefg' is the ancestor, the fragments 'bcd' (from position 2 to 4) to and 'efg' may then be assembled. To do so, all fragments must be presented as matix specifying all start- and end-sites (and fragment-names). buildTree searchs contiguous fragments from columns 'posCo' (start/end) from 'disDat' to build tree & extract path information starting with line 'startFr'. Made for telling if dissociated fragments contribute to long assemblies. This function uses various functions of package data.tree which must be installed, too.

Usage

buildTree(
  disDat,
  startFr = NULL,
  posCo = c("beg", "end"),
  silent = FALSE,
  callFrom = NULL
)

Arguments

disDat

(matrix or data.frame) integer values with 1st column, ie start site of fragment, 2nd column as end of fragments, rownames as unique IDs (node-names)

startFr

(integer) index for 1st node (typically =1 if 'disDat' sorted by "beg"), should point to a terminal node for consective growing of branches

posCo

(character) colnames specifying the begin & start sites in 'disDat', if NULL 1st & 2nd col will be used

silent

(logical) suppress messages

callFrom

(character) allow easier tracking of message(s) produced

Value

list with $paths (branches as matrix with columns 'sumLen' & 'n'), $usedNodes (character vector of all names used to build tree) and $tree (object from data.tree)

See Also

package data.tree original function used Node; in this package : for exploiting edge/tree related issues simpleFragFig, countSameStartEnd and contribToContigPerFrag,

Examples

# NOT RUN {
frag2 <- cbind(beg=c(2,3,7,13,13,15,7,9,7,3,7,5,7,3),end=c(6,12,8,18,20,20,19,12,12,4,12,7,12,4)) 
rownames(frag2) <- c("A","E","B","C","D","F","H","G","I", "J","K","L","M","N")
buildTree(frag2)
countSameStartEnd(frag2)
# }