lefesrCaldes Agglomerates the features abundance at different
taxonomic ranks using mia::splitByRanks
and performs lefser at each rank. The analysis is run at the species,
genus, family, order, class, and phylum levels.
lefserClades(relab, ...)A
(Tree) SummarizedExperiment
with full taxonomy in the rowData @param ... Arguments passed to the
lefser function.
Additional arguments passed to lefser
An object of class 'lefser_df_clades', "lefser_df", and 'data.frame'.
When running lefserClades, all features with NAs in the rowData will
be dropped. This is to avoid creating artificial clades with NAs.
data("zeller14")
z14 <- zeller14[, zeller14$study_condition != "adenoma"]
tn <- get_terminal_nodes(rownames(z14))
z14tn <- z14[tn, ]
z14tn_ra <- relativeAb(z14tn)
z14_input <- rowNames2RowData(z14tn_ra)
resCl <- lefserClades(relab = z14_input, classCol = "study_condition")
#> 18 features don't have species information.
#> 96 features don't have strain information.
#> Dropped 96 features without full taxonomy information.
#> lefser will be run at the kingdom, phylum, class, order, family, genus, species, strain level.
#>
#> >>>> Running lefser at the kingdom level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.
#>
#> >>>> Running lefser at the phylum level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.
#>
#> >>>> Running lefser at the class level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.
#>
#> >>>> Running lefser at the order level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.
#>
#> >>>> Running lefser at the family level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.
#>
#> >>>> Running lefser at the genus level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.
#>
#> >>>> Running lefser at the species level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.
#>
#> >>>> Running lefser at the strain level. <<<<
#> The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
#> See `?factor` or `?relevel` to change the reference category.