finding overlap using GenomicRanges with two data sets specifying minoverlap Function

191 Views Asked by At

I am trying to find overlap using GenomicRanges package function findOverlaps,I have two data sets and want to find overlaps using minoverlap parameter. So I want to give different minoverlap for every read.

Ex df1:

chr2 2800 3270
chr2 3600 4152
chr2 3719 5092
chr2 3893 4547 

Ex. df2 :

chr2 263 20091
chr2 342 17222
chr2 414 2612
chr2 846 4265
chr2L 1030 11575

I want to find overlaps by giving different values of the minOverlap parameter,I have tried something like this but didn't work. The desired output is as usual in genomicRange object.

Example Output:
Hits object with 2 hits and 0 metadata columns:
      queryHits subjectHits
      <integer>   <integer>
  [1]         1           1
  [2]         1           2
  -------
  queryLength: 1 / subjectLength: 10
df11<-toGRanges(df1)
df22<-toGRanges(df2)

minOv<-mapply("-", df1$V3,df1$V2)+1

for (j in minOv) {
    ff<-findOverlaps(query = df11,subject = df22,minoverlap = j)
}

Edit ::

df1::
structure(list(df1c = c("chr2", "chr2", "chr2", "chr2"), df1c2 = c(2800, 
3600, 3719, 3893), df1c3 = c(3270, 4152, 5092, 4547)), class = "data.frame", row.names = c(NA, 
-4L))

df2::

structure(list(df1c = c("chr2", "chr2", "chr2", "chr2", "chr2L"
), df1c2 = c(263, 342, 424, 846, 1030), df1c3 = c(20091, 17222, 
2612, 4265, 11575)), class = "data.frame", row.names = c(NA, 
-5L))

0

There are 0 best solutions below