getCoverage.md
In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

getCoverage works on a 1 sample test dataset

Code
  covFiles
Output
  $Accessibility
  $Accessibility$`C2#PBMCSmall__0.117146`
  GRanges object with 222676 ranges and 1 metadata column:
             seqnames              ranges strand |     score
                <Rle>           <IRanges>  <Rle> | <numeric>
         [1]     chr1            1-521571      * |         0
         [2]     chr1       521572-521598      * |         1
         [3]     chr1       521599-565288      * |         0
         [4]     chr1       565289-565304      * |         1
         [5]     chr1       565305-565335      * |         2
         ...      ...                 ...    ... .       ...
    [222672]     chr2 243040419-243040586      * |         1
    [222673]     chr2 243040587-243041454      * |         0
    [222674]     chr2 243041455-243041513      * |         1
    [222675]     chr2 243041514-243046389      * |         0
    [222676]     chr2 243046390-243046418      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome

  $Accessibility$`C5#PBMCSmall__0.171033`
  GRanges object with 307923 ranges and 1 metadata column:
             seqnames              ranges strand |     score
                <Rle>           <IRanges>  <Rle> | <numeric>
         [1]     chr1            1-565290      * |         0
         [2]     chr1       565291-565293      * |         1
         [3]     chr1       565294-565329      * |         3
         [4]     chr1       565330-565345      * |         2
         [5]     chr1              565346      * |         1
         ...      ...                 ...    ... .       ...
    [307919]     chr2 243031330-243031590      * |         1
    [307920]     chr2 243031591-243034011      * |         0
    [307921]     chr2 243034012-243034339      * |         1
    [307922]     chr2 243034340-243073424      * |         0
    [307923]     chr2 243073425-243073624      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome


  $Insertions
  $Insertions$`C2#PBMCSmall__0.117146`
  GRanges object with 435228 ranges and 1 metadata column:
             seqnames              ranges strand |     score
                <Rle>           <IRanges>  <Rle> | <numeric>
         [1]     chr1            1-521571      * |         0
         [2]     chr1              521572      * |         1
         [3]     chr1       521573-521597      * |         0
         [4]     chr1              521598      * |         1
         [5]     chr1       521599-565288      * |         0
         ...      ...                 ...    ... .       ...
    [435224]     chr2           243041513      * |         1
    [435225]     chr2 243041514-243046389      * |         0
    [435226]     chr2           243046390      * |         1
    [435227]     chr2 243046391-243046417      * |         0
    [435228]     chr2           243046418      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome

  $Insertions$`C5#PBMCSmall__0.171033`
  GRanges object with 587148 ranges and 1 metadata column:
             seqnames              ranges strand |     score
                <Rle>           <IRanges>  <Rle> | <numeric>
         [1]     chr1            1-565290      * |         0
         [2]     chr1              565291      * |         1
         [3]     chr1       565292-565293      * |         0
         [4]     chr1              565294      * |         2
         [5]     chr1       565295-565328      * |         0
         ...      ...                 ...    ... .       ...
    [587144]     chr2           243034339      * |         1
    [587145]     chr2 243034340-243073424      * |         0
    [587146]     chr2           243073425      * |         1
    [587147]     chr2 243073426-243073623      * |         0
    [587148]     chr2           243073624      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome

getCoverage works on a 1 sample test dataset with filterEmpty=TRUE

Code
  covFiles
Output
  $Accessibility
  $Accessibility$`C2#PBMCSmall__0.117146`
  GRanges object with 169007 ranges and 1 metadata column:
             seqnames              ranges strand |     score
                <Rle>           <IRanges>  <Rle> | <numeric>
         [1]     chr1       521572-521598      * |         1
         [2]     chr1       565289-565304      * |         1
         [3]     chr1       565305-565335      * |         2
         [4]     chr1       565336-565349      * |         1
         [5]     chr1       569375-569378      * |         2
         ...      ...                 ...    ... .       ...
    [169003]     chr2 243038802-243038972      * |         1
    [169004]     chr2 243039871-243040072      * |         1
    [169005]     chr2 243040419-243040586      * |         1
    [169006]     chr2 243041455-243041513      * |         1
    [169007]     chr2 243046390-243046418      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome

  $Accessibility$`C5#PBMCSmall__0.171033`
  GRanges object with 258866 ranges and 1 metadata column:
             seqnames              ranges strand |     score
                <Rle>           <IRanges>  <Rle> | <numeric>
         [1]     chr1       565291-565293      * |         1
         [2]     chr1       565294-565329      * |         3
         [3]     chr1       565330-565345      * |         2
         [4]     chr1              565346      * |         1
         [5]     chr1       569387-569412      * |         1
         ...      ...                 ...    ... .       ...
    [258862]     chr2 243031253-243031269      * |         3
    [258863]     chr2 243031270-243031329      * |         2
    [258864]     chr2 243031330-243031590      * |         1
    [258865]     chr2 243034012-243034339      * |         1
    [258866]     chr2 243073425-243073624      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome


  $Insertions
  $Insertions$`C2#PBMCSmall__0.117146`
  GRanges object with 218232 ranges and 1 metadata column:
             seqnames    ranges strand |     score
                <Rle> <IRanges>  <Rle> | <numeric>
         [1]     chr1    521572      * |         1
         [2]     chr1    521598      * |         1
         [3]     chr1    565289      * |         1
         [4]     chr1    565305      * |         1
         [5]     chr1    565335      * |         1
         ...      ...       ...    ... .       ...
    [218228]     chr2 243040586      * |         1
    [218229]     chr2 243041455      * |         1
    [218230]     chr2 243041513      * |         1
    [218231]     chr2 243046390      * |         1
    [218232]     chr2 243046418      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome

  $Insertions$`C5#PBMCSmall__0.171033`
  GRanges object with 296387 ranges and 1 metadata column:
             seqnames        ranges strand |     score
                <Rle>     <IRanges>  <Rle> | <numeric>
         [1]     chr1        565291      * |         1
         [2]     chr1        565294      * |         2
         [3]     chr1        565329      * |         1
         [4]     chr1 565345-565346      * |         1
         [5]     chr1        569387      * |         1
         ...      ...           ...    ... .       ...
    [296383]     chr2     243031590      * |         1
    [296384]     chr2     243034012      * |         1
    [296385]     chr2     243034339      * |         1
    [296386]     chr2     243073425      * |         1
    [296387]     chr2     243073624      * |         1
    -------
    seqinfo: 2 sequences from hg38 genome

getSpecificCoverage works on a 1 sample test dataset

Code
  counts
Output
  $`C2#PBMCSmall__0.117146`
  GRanges object with 2 ranges and 1 metadata column:
        seqnames        ranges strand |     score
           <Rle>     <IRanges>  <Rle> | <numeric>
    [1]     chr1 565291-565349      * |      30.0
    [2]     chr1 569375-569412      * |      30.2
    -------
    seqinfo: 2 sequences from hg38 genome

  $`C5#PBMCSmall__0.171033`
  GRanges object with 4 ranges and 1 metadata column:
        seqnames              ranges strand |     score
           <Rle>           <IRanges>  <Rle> | <numeric>
    [1]     chr1       565291-565346      * |        36
    [2]     chr1       569387-569412      * |        26
    [3]     chr2 243031253-243031590      * |       144
    [4]     chr2 243034012-243034339      * |       328
    -------
    seqinfo: 2 sequences from hg38 genome