Create a long data.frame from a MultiAssayExperiment counts object

This function takes a MultiAssayExperiment object and a specified taxon level of interest and creates a long data.frame that can be used more easily for plotting counts data.

Usage

get_long_data(dat, taxon_level, log = FALSE, counts_to_CPM = FALSE)

Arguments

dat: A MultiAssayExperiment object specially formatted as an animalcules output.
taxon_level: Character string indicating the level of taxonomy to aggregate the counts data. Must be the name of a column in MultiAssayExperiment::rowData(dat).
log: logical. Indicate whether an assay returned should be the log of whichever assay is specified in "output_name". If counts_to_CPM = TRUE as well, then a log CPM assay will also be created. Default is FALSE.
counts_to_CPM: logical. This argument only applies if the input_type is a counts assay. If TRUE, then the output assays will include a normalized CPM assay. If log = TRUE as well, then a log CPM assay will also be created. Default is TRUE.

Value

A data.frame consisting of the counts data, taxa, and metadata.

Examples

in_dat <- system.file("extdata/MAE_small.RDS", package = "LegATo") |> readRDS()
out <- get_long_data(in_dat, "genus", log = TRUE, counts_to_CPM = TRUE)
head(out)
#>           taxon Sample Subject    Sex Month Group Pairing HairLength  Age
#> 1 Acinetobacter    X-1      S1   Male     1     A       1   48.62753 21.9
#> 2 Acinetobacter    X-2      S2   Male     1     B       1   53.53195 67.7
#> 3 Acinetobacter    X-3      S3 Female     1     A       2   47.61090 78.9
#> 4 Acinetobacter    X-4      S4 Female     1     B       2   49.72870 48.6
#> 5 Acinetobacter    X-5      S5 Female     1     A       3   59.04509 48.4
#> 6 Acinetobacter    X-6      S6 Female     1     B       3   27.82404 29.6
#>   Sample_id Abundance
#> 1       X-1      4518
#> 2       X-2     20029
#> 3       X-3    150813
#> 4       X-4       920
#> 5       X-5      1185
#> 6       X-6      2311