diff --git a/book/src/intro_dmr.md b/book/src/intro_dmr.md index a9a5d9b..aa017d2 100644 --- a/book/src/intro_dmr.md +++ b/book/src/intro_dmr.md @@ -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 | samplea counts | counts of each base modification in the region, comma-separated, for sample A | str | -| 7 | samplea total | total number of base modification calls in the region, including unmodified, for sample A | str | -| 8 | sampleb counts | counts of each base modification in the region, comma-separated, for sample B | str | -| 9 | sampleb total | total number of base modification calls in the region, including unmodified, for sample B | str | -| 10 | samplea fractions | fraction of calls for each base modification in the region, comma-separated, for sample A | str | -| 11 | sampleb fractions | fraction of calls for each base modification in the region, comma-separated, for sample B | str | -| 12 | samplea percent modified | percent modification (of any kind) in sample A | float | -| 13 | sampleb 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 | samplea counts | counts of each base modification in the region, comma-separated, for sample A | str | +| 7 | samplea total | total number of base modification calls in the region, including unmodified, for sample A | str | +| 8 | sampleb counts | counts of each base modification in the region, comma-separated, for sample B | str | +| 9 | sampleb total | total number of base modification calls in the region, including unmodified, for sample B | str | +| 10 | samplea percents | percent of calls for each base modification in the region, comma-separated, for sample A | str | +| 11 | sampleb percents | percent of calls for each base modification in the region, comma-separated, for sample B | str | +| 12 | samplea fraction modified | fraction modification (of any kind) in sample A | float | +| 13 | sampleb fraction modified | fraction modification (of any kind) in sample B | float | an example of the output is given below: @@ -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 | samplea counts | counts of each base modification in the region, comma-separated, for sample A | str | -| 8 | sampleb counts | counts of each base modification in the region, comma-separated, for sample B | str | -| 9 | samplea fractions | fraction of calls for each base modification in the region, comma-separated, for sample A | str | -| 10 | sampleb fractions | fraction of calls for each base modification in the region, comma-separated, for sample B | str | -| 11 | samplea percent modified | percent modification (of any kind) in sample A | float | -| 12 | sampleb 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 | samplea counts | counts of each base modification in the region, comma-separated, for sample A | str | +| 8 | sampleb counts | counts of each base modification in the region, comma-separated, for sample B | str | +| 9 | samplea percents | percent of calls for each base modification in the region, comma-separated, for sample A | str | +| 10 | sampleb percents | percent of calls for each base modification in the region, comma-separated, for sample B | str | +| 11 | samplea fraction modified | percent modification (of any kind) in sample A | float | +| 12 | sampleb 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 | diff --git a/docs/intro_dmr.html b/docs/intro_dmr.html index 435aaf4..356fe81 100644 --- a/docs/intro_dmr.html +++ b/docs/intro_dmr.html @@ -330,10 +330,10 @@