countChildrenParent {wrTopDownFrag}

Identify Children/Parent settings as a+b=c

Description

This functions helps identifying fragments ('parent') characterized by a start- and end-position, that got split into 2 'children' fragments. So, each one of the new 'children' conserves either the start- or end-site of the parent and the the remaining ends are on consecutive positions. For example if the sequence 'BCDEFG' (parent) gets split into 'BCD' (positions 1-3) and 'EFG' (positions 4-6), this will be identified as a children/parent 'family' which could be represented as 'a+b=c' case. Note : At this point only settings with 2 children are considered, for more complex scenarions one may build trees using buildTree (however, this function does not identify 'parents'). In proteomics-applications some start- and end-sites may occur multiple times, representing eg unmodified and modified versions of the same basal peptide-sequence. Such duplicated start- and end-cases are handeled as allowed, a 'child' (characterized by its start- and end-position) may occur multiple times, and the corresponding redundant rownames (eg peptide sequence like 'BCD') will be conserved. However, information reflecting eg different peptide modifications must be stored separately. If redudant start- and end-sites accur with different row-names, repeated start- and end-sites will display NA.

Usage

countChildrenParent(
  fragments,
  output = "count",
  silent = FALSE,
  callFrom = NULL
)

Arguments

fragments

(matrix or data.frame) integer values in 1st column, for start site of fragment, and in 2nd column as end-sites of fragments, rownames as IDs

output

(character) choose simply returning results as counts or as list with $counts and $detailIndex (list with details showing each child1,child2 & parent)

silent

(logical) suppress messages

callFrom

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

Value

either numeric vector with cumulated counts (corresponding to rows of fragments) or list with $count and $detailIndex (list with indexes refering to non-redundant entries of all a+b=c settings identified)

See Also

simpleFragFig for graphical representation,countSameStartEnd; for building longer consecutive trees (without identification of 'parent') buildTree and contribToContigPerFrag

Examples

frag3 <- cbind(beg=c(4,2,3,7,13,13,15, 2,9,2,9), end=c(14,6,12,8,18,20,20, 8,12,12,18)) 
rownames(frag3) <- c("K","A","E","B","C","D","F", "H","G","I","J")
countChildrenParent(frag3)
## example with duplicate start- and end-position positions
frag3c <- cbind(beg=c(4,2,3,7, 7,13, 13,13,15, 2,9,2,9,9),
  end=c(14,6,12,8, 8,18, 18,20,20, 8,12,12,12,18))
rownames(frag3c) <- c("K","A","E", "B","B", "C","C","D","F", "H","G","I","G","J")
countChildrenParent(frag3c, out="det")