example.R

> head(cage)
GRanges object with 6 ranges and 1 metadata column:
      seqnames               ranges strand |       tpm
         <Rle>            <IRanges>  <Rle> | <numeric>
  [1]    chr22 [42017258, 42017373]      + |  534.6991
  [2]    chr22 [24236548, 24236627]      + |  640.9699
  [3]    chr21 [34915313, 34915452]      + |  461.0562
  [4]    chr22 [18111391, 18111584]      - |  403.6615
  [5]    chr22 [38071637, 38071688]      + |  450.2464
  [6]    chr22 [36783979, 36784055]      - |  373.9197
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> head(promoters)
GRanges object with 6 ranges and 0 metadata columns:
      seqnames               ranges strand
         <Rle>            <IRanges>  <Rle>
  [1]    chr21 [42218039, 42220039]      -
  [2]    chr21 [17441841, 17443841]      +
  [3]    chr21 [17565698, 17567698]      +
  [4]    chr21 [30395937, 30397937]      +
  [5]    chr21 [27542138, 27544138]      -
  [6]    chr21 [27511708, 27513708]      -
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

sm <- ScoreMatrix(target=cage, windows=pro> sm
> sm
  scoreMatrix with dims: 1055 2001