diff --git a/README.md b/README.md index dde183a..1fb86db 100644 --- a/README.md +++ b/README.md @@ -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. diff --git a/man/maaslin_write_results.Rd b/man/maaslin_write_results.Rd index 624f841..ed4875f 100644 --- a/man/maaslin_write_results.Rd +++ b/man/maaslin_write_results.Rd @@ -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. diff --git a/vignettes/maaslin3_manual.Rmd b/vignettes/maaslin3_manual.Rmd index f3b5d4d..9b9680b 100644 --- a/vignettes/maaslin3_manual.Rmd +++ b/vignettes/maaslin3_manual.Rmd @@ -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. diff --git a/vignettes/maaslin3_tutorial.Rmd b/vignettes/maaslin3_tutorial.Rmd index fa9f8a2..e628eee 100644 --- a/vignettes/maaslin3_tutorial.Rmd +++ b/vignettes/maaslin3_tutorial.Rmd @@ -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: