How to generate input file for Bioconductor package heatmaps
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bony.dekumar ▴ 10
@bonydekumar-19283
Last seen 22 months ago
United States

Hi all, I am new to heatmap package . I have ChIP-Seq data and called peaks using Macs2. I have a corresponding bam files. How to generate input suitable for bioconductor package heatmaps. looking at example it looks like following

head(h3k4me3_30p_pos)
RleList of length 6
$chr1
numeric-Rle of length 60348388 with 81975 runs
  Lengths: 53048     4     3     2     2 ...     1     2   227    13  1029
  Values :     0     4     6    10    14 ...     5     6     0     1     0

$chr10
numeric-Rle of length 46591166 with 72219 runs
  Lengths: 31086    36    60     4    11 ...     2     1     2     1 41953
  Values :     0     7     0     2     4 ...     3     5     0     1     0

$chr11
numeric-Rle of length 46661319 with 65746 runs
  Lengths: 44601    36    27    36   286 ...     3     1    10     3 33899
  Values :     0     1     0     5     0 ...     3     2     0     1     0

$chr12
numeric-Rle of length 50697278 with 63411 runs
  Lengths:  9278    34     2    11    12 ...     1     2     3     1 14636
  Values :     0     2     3     0     1 ...    11     8     4     1     0

$chr13
numeric-Rle of length 54093808 with 80461 runs
  Lengths:    490     15      6      5     63 ...     82      3      1 104575
  Values :      0      1      0      1      0 ...      0      3      2      0

...
<1 more element>

How i could convert my peak data into this format.

Thanks

heatmaps input file • 862 views
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