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Modeling for Single-Cell Open Chromatin Analysis

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tests/testthat/_snaps/3sample/annotateTiles.md

tests/testthat/_snaps/3sample/annotateTiles.md
In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

annotateTiles works on a 3 sample test dataset

Code
  SummarizedExperiment::rowRanges(STM)
Output
  GRanges object with 22773 ranges and 4 metadata columns:
                              seqnames              ranges strand |        C2
                                 <Rle>           <IRanges>  <Rle> | <logical>
    chr10:100028000-100028499    chr10 100028000-100028499      * |      TRUE
    chr10:100080500-100080999    chr10 100080500-100080999      * |     FALSE
    chr10:100147000-100147499    chr10 100147000-100147499      * |     FALSE
    chr10:100227000-100227499    chr10 100227000-100227499      * |     FALSE
    chr10:101190000-101190499    chr10 101190000-101190499      * |      TRUE
                          ...      ...                 ...    ... .       ...
       chrX:99870000-99870499     chrX   99870000-99870499      * |     FALSE
       chrY:16263500-16263999     chrY   16263500-16263999      * |     FALSE
       chrY:21154500-21154999     chrY   21154500-21154999      * |     FALSE
         chrY:2709500-2709999     chrY     2709500-2709999      * |     FALSE
         chrY:2803000-2803499     chrY     2803000-2803499      * |     FALSE
                                     C3    tileType        Gene
                              <logical> <character> <character>
    chr10:100028000-100028499     FALSE    Promoter       LOXL4
    chr10:100080500-100080999      TRUE      Distal        <NA>
    chr10:100147000-100147499      TRUE  Intragenic     PYROXD2
    chr10:100227000-100227499      TRUE  Intragenic       HPSE2
    chr10:101190000-101190499     FALSE    Promoter        GOT1
                          ...       ...         ...         ...
       chrX:99870000-99870499      TRUE      Distal        <NA>
       chrY:16263500-16263999      TRUE      Distal        <NA>
       chrY:21154500-21154999      TRUE    Promoter        CD24
         chrY:2709500-2709999      TRUE    Promoter      RPS4Y1
         chrY:2803000-2803499      TRUE    Promoter         ZFY
    -------
    seqinfo: 24 sequences from an unspecified genome; no seqlengths

annotateTiles works on a GRanges

Code
  ranges
Output
  GRanges object with 22773 ranges and 4 metadata columns:
                              seqnames              ranges strand |        C2
                                 <Rle>           <IRanges>  <Rle> | <logical>
    chr10:100028000-100028499    chr10 100028000-100028499      * |      TRUE
    chr10:100080500-100080999    chr10 100080500-100080999      * |     FALSE
    chr10:100147000-100147499    chr10 100147000-100147499      * |     FALSE
    chr10:100227000-100227499    chr10 100227000-100227499      * |     FALSE
    chr10:101190000-101190499    chr10 101190000-101190499      * |      TRUE
                          ...      ...                 ...    ... .       ...
       chrX:99870000-99870499     chrX   99870000-99870499      * |     FALSE
       chrY:16263500-16263999     chrY   16263500-16263999      * |     FALSE
       chrY:21154500-21154999     chrY   21154500-21154999      * |     FALSE
         chrY:2709500-2709999     chrY     2709500-2709999      * |     FALSE
         chrY:2803000-2803499     chrY     2803000-2803499      * |     FALSE
                                     C3    tileType        Gene
                              <logical> <character> <character>
    chr10:100028000-100028499     FALSE      Distal        <NA>
    chr10:100080500-100080999      TRUE  Intragenic        CPN1
    chr10:100147000-100147499      TRUE      Distal        <NA>
    chr10:100227000-100227499      TRUE  Intragenic        CHUK
    chr10:101190000-101190499     FALSE  Intragenic   LINC01514
                          ...       ...         ...         ...
       chrX:99870000-99870499      TRUE      Distal        <NA>
       chrY:16263500-16263999      TRUE      Distal        <NA>
       chrY:21154500-21154999      TRUE      Distal        <NA>
         chrY:2709500-2709999      TRUE  Intragenic        CD99
         chrY:2803000-2803499      TRUE      Distal        <NA>
    -------
    seqinfo: 24 sequences from an unspecified genome; no seqlengths


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MOCHA documentation built on May 29, 2024, 2:25 a.m.

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