Run lefser at different clades

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, ...)

Arguments

relab

A (Tree) SummarizedExperiment with full taxonomy in the rowData.

...

Arguments passed to the lefser function.

Value

An object of class 'lefser_df_clades', "lefser_df", and 'data.frame'.

Details

When running lefserClades, all features with NAs in the rowData will be dropped. This is to avoid creating artificial clades with NAs.

Examples

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.