Hi Aaron,

I tried to use plotDI, but it occurs error as following:

> plotDI(iset, test.fc,  first.region=GRanges("chr1", IRanges(22240001, 22280000)), second.region=GRanges("chr1", IRanges(3000001, 3040000)), diag=FALSE)
Error in if (first.min > first.max || second.min > second.max) { :
  missing value where TRUE/FALSE needed
 

Would you help me how to figure it out? Thanks.
 

I would guess that you haven't constructed iset properly, i.e., it doesn't contain sequence length information for chromosome 1. If you tried something like seqlengths(regions(iset))[["chr1"]], do you get a sensible value? It's probably NA instead, which leads to the observed error above.

I used method you posted at Loading a precomputed interaction matrix into diffHiC for iset file generation

------------------------------------------

> library(rtracklayer)
> bin.coords <- import("bin_4k.bed")
> bin.coords <- as(bin.coords, "GRanges")
> head(bin.coords)
GRanges object with 6 ranges and 0 metadata columns:
      seqnames           ranges strand
         <Rle>        <IRanges>  <Rle>
  [1]     chr1 [     1,  40000]      *
  [2]     chr1 [ 40001,  80000]      *
  [3]     chr1 [ 80001, 120000]      *
  [4]     chr1 [120001, 160000]      *
  [5]     chr1 [160001, 200000]      *
  [6]     chr1 [200001, 240000]      *
  -------
  seqinfo: 22 sequences from an unspecified genome; no seqlengths
> library(InteractionSet)
> a_40000.matrix <-read.table("a_40000.matrix")
> gi <- GInteractions(a_40000.matrix[,1], a_40000.matrix[,2], bin.coords, mode="reverse")
> head(gi)
ReverseStrictGInteractions object with 6 interactions and 0 metadata columns:
      seqnames1            ranges1     seqnames2            ranges2
          <Rle>          <IRanges>         <Rle>          <IRanges>
  [1]      chr1 [3000001, 3040000] ---      chr1 [3000001, 3040000]
  [2]      chr1 [3040001, 3080000] ---      chr1 [3000001, 3040000]
  [3]      chr1 [3080001, 3120000] ---      chr1 [3000001, 3040000]
  [4]      chr1 [3120001, 3160000] ---      chr1 [3000001, 3040000]
  [5]      chr1 [3160001, 3200000] ---      chr1 [3000001, 3040000]
  [6]      chr1 [3200001, 3240000] ---      chr1 [3000001, 3040000]
  -------
  regions: 68149 ranges and 0 metadata columns
  seqinfo: 22 sequences from an unspecified genome; no seqlengths

> iset<-InteractionSet(as.matrix(a_40000.matrix[,3]), gi)
> seqlengths(regions(iset))[["chr1"]]
[1] NA
> seqlengths(regions(iset))
 chr1  chr2  chr3  chr4  chr5  chr6  chr7  chr8  chr9 chr10 chr11 chr12 chr13
   NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA
chr14 chr15 chr16 chr17 chr18 chr19  chrX  chrY  chrM
   NA    NA    NA    NA    NA    NA    NA    NA    NA
----------------------------------------------------------------

Like what you guessed, seqlengths(regions(iset))[["chr1"]]. how can I fix it? Thanks.