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Merge branch 'master' of https://github.com/biobakery/Maaslin3
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WillNickols committed Nov 15, 2024

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4 changes: 2 additions & 2 deletions README.md
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@@ -179,8 +179,8 @@ contains all the data and results (see `?maaslin_fit`).
number of non-zero data points for the feature.
* ``significant_results.tsv``
* This file is a subset of the results in the first file.
* It only includes associations with q-values <= to the threshold and no
errors.
* It only includes associations with joint or individual q-values less
than or equal to the threshold and no errors.
* ``features``
* This folder includes the filtered, normalized, and transformed
versions of the input feature table.
3 changes: 2 additions & 1 deletion man/maaslin_write_results.Rd
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@@ -35,7 +35,8 @@ file \code{all_results.tsv} will contain all results in the
\code{fit_data_abundance} and \code{fit_data_prevalence} items of the
input list (with 'linear' and 'logistic' replaced by 'abundance' and
'prevalence' in the \code{model} column). The file
\code{significant_results.tsv} will contain all results with joint
\code{significant_results.tsv} will contain all results with joint or
individual
q-values below the `max_significance` parameter and only `NA` in the
`error` column of the results (the `error` column is subsequently
dropped). No value is returned.
4 changes: 2 additions & 2 deletions vignettes/maaslin3_manual.Rmd
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@@ -196,8 +196,8 @@ contains all the data and results (see `?maaslin_fit`).
number of non-zero data points for the feature.
* ``significant_results.tsv``
* This file is a subset of the results in the first file.
* It only includes associations with joint q-values <= to the threshold
and no errors.
* It only includes associations with joint or individual q-values less
than or equal to the threshold and no errors.
* ``features``
* This folder includes the filtered, normalized, and transformed
versions of the input feature table.
3 changes: 2 additions & 1 deletion vignettes/maaslin3_tutorial.Rmd
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@@ -355,7 +355,8 @@ supplying spike-in or total abundances with `unscaled_abundance`.
#### Significant associations

The main output from MaAsLin 3 is the list of significant associations
in `significant_results.tsv`. This lists all associations with joint q-values
in `significant_results.tsv`. This lists all associations with joint
or individual q-values
that pass MaAsLin 3's significance
threshold, ordered by increasing individual q-value. The format is:

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