From 4c14724b4ba87cb08743d623e0730ca0386f9d00 Mon Sep 17 00:00:00 2001 From: Lukas Kremer Date: Mon, 7 Oct 2024 15:36:41 +0200 Subject: [PATCH] update docs --- docs/commands.md | 48 ++++++++++++++++++++++++++-------------- docs/make_commands_md.sh | 16 +++++++------- 2 files changed, 39 insertions(+), 25 deletions(-) diff --git a/docs/commands.md b/docs/commands.md index 14a014b..45dd8f8 100644 --- a/docs/commands.md +++ b/docs/commands.md @@ -2,18 +2,23 @@ ``` 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: @@ -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. @@ -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. @@ -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 @@ -279,10 +293,10 @@ Options: 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. ``` diff --git a/docs/make_commands_md.sh b/docs/make_commands_md.sh index ce97a99..908fd47 100755 --- a/docs/make_commands_md.sh +++ b/docs/make_commands_md.sh @@ -1,25 +1,25 @@ #!/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