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[docs] gh223, part 2
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@ArtRand
ArtRand committed Jul 2, 2024
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60 changes: 30 additions & 30 deletions book/src/intro_dmr.md
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Expand Up @@ -172,21 +172,21 @@ If your bedMethyl has records with custom modification codes or codes that aren'
The output from `modkit dmr pair` (and for each pairwise comparison with `modkit dmr multi`) is (roughly)
a BED file with the following schema:

| column | name | description | type |
|--------|-------------------------------------|-------------------------------------------------------------------------------------------|-------|
| 1 | chrom | name of reference sequence from bedMethyl input samples | str |
| 2 | start position | 0-based start position, from `--regions` argument | int |
| 3 | end position | 0-based exclusive end position, from `--regions` argument | int |
| 4 | name | `name` column from `--regions` BED, or `chr:start-stop` if absent | str |
| 5 | score | difference score, more positive values have increased difference | float |
| 6 | sample<sub>a</sub> counts | counts of each base modification in the region, comma-separated, for sample A | str |
| 7 | sample<sub>a</sub> total | total number of base modification calls in the region, including unmodified, for sample A | str |
| 8 | sample<sub>b</sub> counts | counts of each base modification in the region, comma-separated, for sample B | str |
| 9 | sample<sub>b</sub> total | total number of base modification calls in the region, including unmodified, for sample B | str |
| 10 | sample<sub>a</sub> fractions | fraction of calls for each base modification in the region, comma-separated, for sample A | str |
| 11 | sample<sub>b</sub> fractions | fraction of calls for each base modification in the region, comma-separated, for sample B | str |
| 12 | sample<sub>a</sub> percent modified | percent modification (of any kind) in sample A | float |
| 13 | sample<sub>b</sub> percent modified | percent modification (of any kind) in sample B | float |
| column | name | description | type |
|--------|--------------------------------------|-------------------------------------------------------------------------------------------|-------|
| 1 | chrom | name of reference sequence from bedMethyl input samples | str |
| 2 | start position | 0-based start position, from `--regions` argument | int |
| 3 | end position | 0-based exclusive end position, from `--regions` argument | int |
| 4 | name | `name` column from `--regions` BED, or `chr:start-stop` if absent | str |
| 5 | score | difference score, more positive values have increased difference | float |
| 6 | sample<sub>a</sub> counts | counts of each base modification in the region, comma-separated, for sample A | str |
| 7 | sample<sub>a</sub> total | total number of base modification calls in the region, including unmodified, for sample A | str |
| 8 | sample<sub>b</sub> counts | counts of each base modification in the region, comma-separated, for sample B | str |
| 9 | sample<sub>b</sub> total | total number of base modification calls in the region, including unmodified, for sample B | str |
| 10 | sample<sub>a</sub> percents | percent of calls for each base modification in the region, comma-separated, for sample A | str |
| 11 | sample<sub>b</sub> percents | percent of calls for each base modification in the region, comma-separated, for sample B | str |
| 12 | sample<sub>a</sub> fraction modified | fraction modification (of any kind) in sample A | float |
| 13 | sample<sub>b</sub> fraction modified | fraction modification (of any kind) in sample B | float |

an example of the output is given below:

Expand Down Expand Up @@ -270,19 +270,19 @@ To activate "fine-grained" mode, pass the `--fine-grained` flag.

The output schema for the segments is:

| column | name | description | type |
|--------|-------------------------------------|-------------------------------------------------------------------------------------------|-------|
| 1 | chrom | name of reference sequence from bedMethyl input samples | str |
| 2 | start position | 0-based start position, from `--regions` argument | int |
| 3 | end position | 0-based exclusive end position, from `--regions` argument | int |
| 4 | state-name | "different" when sites are differentially modified, "same" otherwise | str |
| 5 | score | difference score, more positive values have increased difference | float |
| 6 | N-sites | number of sites (bedmethyl records) in the segment | float |
| 7 | sample<sub>a</sub> counts | counts of each base modification in the region, comma-separated, for sample A | str |
| 8 | sample<sub>b</sub> counts | counts of each base modification in the region, comma-separated, for sample B | str |
| 9 | sample<sub>a</sub> fractions | fraction of calls for each base modification in the region, comma-separated, for sample A | str |
| 10 | sample<sub>b</sub> fractions | fraction of calls for each base modification in the region, comma-separated, for sample B | str |
| 11 | sample<sub>a</sub> percent modified | percent modification (of any kind) in sample A | float |
| 12 | sample<sub>b</sub> percent modified | percent modification (of any kind) in sample B | float |
| 13 | effect size | percent modified in sample A (col 11) minus percent modified in sample B (col 12) | float |
| column | name | description | type |
|--------|--------------------------------------|-------------------------------------------------------------------------------------------|-------|
| 1 | chrom | name of reference sequence from bedMethyl input samples | str |
| 2 | start position | 0-based start position, from `--regions` argument | int |
| 3 | end position | 0-based exclusive end position, from `--regions` argument | int |
| 4 | state-name | "different" when sites are differentially modified, "same" otherwise | str |
| 5 | score | difference score, more positive values have increased difference | float |
| 6 | N-sites | number of sites (bedmethyl records) in the segment | float |
| 7 | sample<sub>a</sub> counts | counts of each base modification in the region, comma-separated, for sample A | str |
| 8 | sample<sub>b</sub> counts | counts of each base modification in the region, comma-separated, for sample B | str |
| 9 | sample<sub>a</sub> percents | percent of calls for each base modification in the region, comma-separated, for sample A | str |
| 10 | sample<sub>b</sub> percents | percent of calls for each base modification in the region, comma-separated, for sample B | str |
| 11 | sample<sub>a</sub> fraction modified | percent modification (of any kind) in sample A | float |
| 12 | sample<sub>b</sub> fraction modified | percent modification (of any kind) in sample B | float |
| 13 | effect size | percent modified in sample A (col 11) minus percent modified in sample B (col 12) | float |

16 changes: 8 additions & 8 deletions docs/intro_dmr.html
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Expand Up @@ -330,10 +330,10 @@ <h2 id="differential-methylation-output-format"><a class="header" href="#differe
<tr><td>7</td><td>sample<sub>a</sub> total</td><td>total number of base modification calls in the region, including unmodified, for sample A</td><td>str</td></tr>
<tr><td>8</td><td>sample<sub>b</sub> counts</td><td>counts of each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>9</td><td>sample<sub>b</sub> total</td><td>total number of base modification calls in the region, including unmodified, for sample B</td><td>str</td></tr>
<tr><td>10</td><td>sample<sub>a</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>b</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>12</td><td>sample<sub>a</sub> percent modified</td><td>percent modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>13</td><td>sample<sub>b</sub> percent modified</td><td>percent modification (of any kind) in sample B</td><td>float</td></tr>
<tr><td>10</td><td>sample<sub>a</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>b</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>12</td><td>sample<sub>a</sub> fraction modified</td><td>fraction modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>13</td><td>sample<sub>b</sub> fraction modified</td><td>fraction modification (of any kind) in sample B</td><td>float</td></tr>
</tbody></table>
</div>
<p>an example of the output is given below:</p>
Expand Down Expand Up @@ -407,10 +407,10 @@ <h2 id="segmenting-on-differential-methylation"><a class="header" href="#segment
<tr><td>6</td><td>N-sites</td><td>number of sites (bedmethyl records) in the segment</td><td>float</td></tr>
<tr><td>7</td><td>sample<sub>a</sub> counts</td><td>counts of each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>8</td><td>sample<sub>b</sub> counts</td><td>counts of each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>9</td><td>sample<sub>a</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>10</td><td>sample<sub>b</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>a</sub> percent modified</td><td>percent modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>12</td><td>sample<sub>b</sub> percent modified</td><td>percent modification (of any kind) in sample B</td><td>float</td></tr>
<tr><td>9</td><td>sample<sub>a</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>10</td><td>sample<sub>b</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>a</sub> fraction modified</td><td>percent modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>12</td><td>sample<sub>b</sub> fraction modified</td><td>percent modification (of any kind) in sample B</td><td>float</td></tr>
<tr><td>13</td><td>effect size</td><td>percent modified in sample A (col 11) minus percent modified in sample B (col 12)</td><td>float</td></tr>
</tbody></table>
</div>
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16 changes: 8 additions & 8 deletions docs/print.html
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Expand Up @@ -919,10 +919,10 @@ <h2 id="differential-methylation-output-format"><a class="header" href="#differe
<tr><td>7</td><td>sample<sub>a</sub> total</td><td>total number of base modification calls in the region, including unmodified, for sample A</td><td>str</td></tr>
<tr><td>8</td><td>sample<sub>b</sub> counts</td><td>counts of each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>9</td><td>sample<sub>b</sub> total</td><td>total number of base modification calls in the region, including unmodified, for sample B</td><td>str</td></tr>
<tr><td>10</td><td>sample<sub>a</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>b</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>12</td><td>sample<sub>a</sub> percent modified</td><td>percent modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>13</td><td>sample<sub>b</sub> percent modified</td><td>percent modification (of any kind) in sample B</td><td>float</td></tr>
<tr><td>10</td><td>sample<sub>a</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>b</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>12</td><td>sample<sub>a</sub> fraction modified</td><td>fraction modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>13</td><td>sample<sub>b</sub> fraction modified</td><td>fraction modification (of any kind) in sample B</td><td>float</td></tr>
</tbody></table>
</div>
<p>an example of the output is given below:</p>
Expand Down Expand Up @@ -996,10 +996,10 @@ <h2 id="segmenting-on-differential-methylation"><a class="header" href="#segment
<tr><td>6</td><td>N-sites</td><td>number of sites (bedmethyl records) in the segment</td><td>float</td></tr>
<tr><td>7</td><td>sample<sub>a</sub> counts</td><td>counts of each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>8</td><td>sample<sub>b</sub> counts</td><td>counts of each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>9</td><td>sample<sub>a</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>10</td><td>sample<sub>b</sub> fractions</td><td>fraction of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>a</sub> percent modified</td><td>percent modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>12</td><td>sample<sub>b</sub> percent modified</td><td>percent modification (of any kind) in sample B</td><td>float</td></tr>
<tr><td>9</td><td>sample<sub>a</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample A</td><td>str</td></tr>
<tr><td>10</td><td>sample<sub>b</sub> percents</td><td>percent of calls for each base modification in the region, comma-separated, for sample B</td><td>str</td></tr>
<tr><td>11</td><td>sample<sub>a</sub> fraction modified</td><td>percent modification (of any kind) in sample A</td><td>float</td></tr>
<tr><td>12</td><td>sample<sub>b</sub> fraction modified</td><td>percent modification (of any kind) in sample B</td><td>float</td></tr>
<tr><td>13</td><td>effect size</td><td>percent modified in sample A (col 11) minus percent modified in sample B (col 12)</td><td>float</td></tr>
</tbody></table>
</div><div style="break-before: page; page-break-before: always;"></div><h1 id="validating-ground-truth-results"><a class="header" href="#validating-ground-truth-results">Validating ground truth results.</a></h1>
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2 changes: 1 addition & 1 deletion docs/searchindex.js
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