Empty matrix

[michela12345]

I try to do a matrix for plotting a EnrichHeatmap but with the command normalizeToMatrix I have a matrix with only zero (when I plot the EnrichHeatmap is white) and I don't understand which is the problem, can someone help me?

tss <- getPromoters(TxDb=txdb, upstream=500, downstream=500)
tss[1:3]

GRanges object with 3 ranges and 0 metadata columns:
      seqnames          ranges strand
         <Rle>       <IRanges>  <Rle>
  [1]     chrI 5107333-5108333      +
  [2]    chrIV 9601195-9602195      -
  [3]     chrV 9245860-9246860      -

intestine_gr <- makeGRangesFromDataFrame(intestine, keep.extra.columns = TRUE)
intestine_gr[1:3]

GRanges object with 3 ranges and 14 metadata columns:

       seqnames    ranges strand |                     V4                                V5          
          <Rle> <IRanges>  <Rle> |            <character>                <numeric>       
      7015     chrX   9838425      * | peak_C1_H3K4me3_peak..          5.19002          
         653     chrI   7602023      * | peak_C1_H3K4me3_peak..         15.02140          
       6284     chrX    760757      * | peak_C1_H3K4me3_peak..           7.93376

mat1 <- normalizeToMatrix(intestine_gr, tss, value_column = "V5", extend = 5000, mean_mode = "w0", w = 50)

> mat1
Normalize intestine_gr to tss:
  Upstream 5000 bp (100 windows)
  Downstream 5000 bp (100 windows)
  Include target regions (44 windows)
  61451 target regions

[jokergoo]

It would be better if you also provide your dataset.