Deconvoluting intervals into position information

Question

I have fileA in which the information is displayed by intervals - if consecutive positions are assigned the same value, these consecutive values are regrouped into one interval.

start     end      value    label
123       78000    0        romeo    #value 0 at positions 123 to 77999 included.
78000     78004    56       romeo    #value 56 at positions 78000, 78001, 78002 and 78003.
78004     78005    12       romeo    #value 12 at position 78004.
78006     78008    21       juliet   #value 21 at positions 78006 and 78007.
78008     78056    8        juliet   #value 8 at positions 78008 to 78055 included.

The intervals I am interested in are displayed in fileB:

start     end      label
77998     78005    romeo
78007     78012    juliet

[EDIT] The labels in fileA were originally pulled in from fileB, so it is safe to assume that the labels are always equivalent for overlapping intervals.

I am trying to extract the information for all the individual positions corresponding to the intervals in the second file, a process that I will call "deconvolution" for lack of a better word. The output fileC should come up like this:

position  value   label
77998     0       romeo
77999     0       romeo
78000     56      romeo
78001     56      romeo
78002     56      romeo
78003     56      romeo
78004     12      romeo   
78007     21      juliet
78008     8       juliet
78009     8       juliet
78010     8       juliet
78011     8       juliet

This is my code:

#read from tab-delimited text files which do not contain column names
A<-read.table("fileA.txt",sep="\t",colClasses=c("numeric","numeric","numeric","character"))
B<-read.table("fileB.txt",sep="\t",colClasses=c("numeric","numeric","character"))
#create empty table.frame for the output
C <- data.frame (1,2,3)
C <- C[-1,]

#add column names
colnames(A)<-c("start","end","value","label")
colnames(B)<-c("start","end","label")
colnames(C)<-c("position","value","label")

#extract position information
deconvolute <- function(x,y,z) {
    for x$label %in% y$label {
        #compute sequence of overlapping positions
        overlap<-seq(max(x$start,y$start),x$end,1)
        z$position<-overlap
        #assign corresponding values to the other columns
        z$value<-rep(x$value,length(overlap))
        z$label<-rep(x$label,length(overlap))
        }
    }

deconvolute(A,B,C)

I am getting a lot of syntax errors in my function. I would be very happy if someone could help me fix them.

Answer 1

# create sequence of positions
s <- unlist(apply(B, MARGIN=1, FUN=function(x) seq(x[1], as.numeric(x[2])-1)))
s
 [1] 77998 77999 78000 78001 78002 78003 78004 78007 78008 78009 78010 78011

# matching between files A and B

pos <- unlist(sapply(s, FUN=function(x)
  which(
         apply(A, MARGIN=1, FUN=function(y) as.numeric(y[1])<=as.numeric(x) & as.numeric(x) < as.numeric(y[2])))
       ))

# new dataframe
deconvoluted <- data.frame(s, A$value[pos], A$label[pos])
deconvoluted 

      s A.value.pos. A.label.pos.
1  77998            0        romeo
2  77999            0        romeo
3  78000           56        romeo
4  78001           56        romeo
5  78002           56        romeo
6  78003           56        romeo
7  78004           12        romeo
8  78007           21       juliet
9  78008            8       juliet
10 78009            8       juliet
11 78010            8       juliet
12 78011            8       juliet