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update docs
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@LKremer
LKremer committed Oct 7, 2024
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48 changes: 31 additions & 17 deletions docs/commands.md
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```
Usage: methscan [OPTIONS] COMMAND [ARGS]...
MethSCAn version 1.0.0
__ __ _ _ ____ ____ _ 
| \/ | ___| |_| |__ / ___| / ___| / \ _ __
| |\/| |/ _ \ __| '_ \\___ \| | / _ \ | '_ \ 
| | | | __/ |_| | | |___) | |___ / ___ \| | | |
|_| |_|\___|\__|_| |_|____/ \____/_/ \_\_| |_| v1.0.2
Below you find a list of all available commands. To find out what they do
and how to use them, check their help like this:
Below you find a list of all available commands. To find out what they do
and how to use them, check their help like this:
methscan [command] --help
methscan [command] --help
To use stdin or stdout, use the dash character - instead of a file
path.
For documentation and a usage tutorial, go to
https://anders-biostat.github.io/MethSCAn/.
Options:
--version Show the version and exit.
--cite Show publication reference and exit.
--help Show this message and exit.
Commands:
Expand Down Expand Up @@ -150,16 +155,20 @@ Options:
Increase this value to find larger VMRs.
[default: 2000; x>=1]
--stepsize INTEGER Step size of the sliding window in basepairs.
Increase this value to gain speed, at the cost of
some accuracy. [default: 100; x>=1]
Should be smaller than the bandwidth. Increase
this value to gain speed, at the cost of some
accuracy. [default: 100; x>=1]
--var-threshold FLOAT The variance threshold, i.e. 0.02 means that the
top 2% most variable genomic bins will be
reported. Overlapping variable bins are merged.
[default: 0.02; 0<=x<=1]
top 2% most variable genomic bins will be merged
and reported as VMRs. [default: 0.02; 0<=x<=1]
--min-cells INTEGER The minimum number of cells required to report a
VMR. For example, a value of 6 means that only
VMRs with sequencing coverage in at least 6 cells
are reported. [default: 6; x>=1]
--bridge-gaps INTEGER Merge neighboring VMRs if they are within this
distance in basepairs. Useful to prevent
fragmented VMRs separated only by small gaps.
[default: off] [x>=0]
--threads INTEGER How many CPU threads to use in parallel.
[default: all available]
--write-header Write the column names of the output file.
Expand Down Expand Up @@ -202,14 +211,19 @@ Options:
Increase this value to gain speed, at the cost of
some accuracy. [default: 1000; x>=1]
--threshold FLOAT The t-statistic threshold, i.e. 0.02 means that
the top 2% most differentially methylated genomic
bins will be reported. Overlapping bins are
merged. [default: 0.02; 0<=x<=1]
the top 2% and bottom 2% most differentially
methylated genomic bins will be separately merged
and reported as DMRs with adjusted p-values.
[default: 0.02; 0<=x<=1]
--min-cells INTEGER The minimum number of cells required to consider a
genomic region for testing. For example, a value
of 6 means that only regions with sequencing
coverage in at least 6 cells per group are
considered. [default: 6; x>=1]
--bridge-gaps INTEGER Merge neighboring DMRs if they are within this
distance in basepairs. Useful to prevent
fragmented DMRs separated only by small gaps.
[default: off] [x>=0]
--threads INTEGER How many CPU threads to use in parallel.
[default: all available]
--write-header Write the column names of the output file.
Expand Down Expand Up @@ -246,7 +260,7 @@ Usage: methscan matrix [OPTIONS] REGIONS DATA_DIR OUTPUT_DIR
Options:
--sparse [experimental] Write the output as a sparse matrix,
instead of the four .csv.gz files described above. This
is faster and more space-efficient for large data sets.
is faster and more space-efficient for huge data sets.
The output 'matrix.mtx.gz' contains four columns:
row_index, col_index, shrunken residuals, methylation
fractions, coverage. Both indices are 1-indexed. Missing
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will be extended, longer regions will be shortened
accordingly. [default: 4000; x>=1]
--strand-column INTEGER The bed column number (1-indexed) denoting the DNA
strand of the region [optional]. [x>=1]
strand of the region. [optional] [x>=1]
--label TEXT Specify a constant value to be added as a column to
the output table. This can be useful to give each
output a unique label when you want to concatenate
multiple outputs [optional].
multiple outputs. [optional]
--help Show this message and exit.
```
16 changes: 8 additions & 8 deletions docs/make_commands_md.sh
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#!/usr/bin/env sh

echo -e "# List of available commands\n\`\`\`" > commands.md
methscan --help >> commands.md
poetry run methscan --help >> commands.md
echo -e "\`\`\`\n# prepare\n\`\`\`" >> commands.md
methscan prepare --help >> commands.md
poetry run methscan prepare --help >> commands.md

echo -e "\`\`\`\n# filter\n\`\`\`" >> commands.md
methscan filter --help >> commands.md
poetry run methscan filter --help >> commands.md

echo -e "\`\`\`\n# smooth\n\`\`\`" >> commands.md
methscan smooth --help >> commands.md
poetry run methscan smooth --help >> commands.md

echo -e "\`\`\`\n# scan\n\`\`\`" >> commands.md
methscan scan --help >> commands.md
poetry run methscan scan --help >> commands.md

echo -e "\`\`\`\n# diff\n\`\`\`" >> commands.md
methscan diff --help >> commands.md
poetry run methscan diff --help >> commands.md

echo -e "\`\`\`\n# matrix\n\`\`\`" >> commands.md
methscan matrix --help >> commands.md
poetry run methscan matrix --help >> commands.md

echo -e "\`\`\`\n# profile\n\`\`\`" >> commands.md
methscan profile --help >> commands.md
poetry run methscan profile --help >> commands.md
echo -e "\`\`\`" >> commands.md

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