Create the microbiome_dataset object.
create_microbiome_dataset(
expression_data,
sample_info,
variable_info,
otu_tree,
taxa_tree,
ref_seq,
sample_info_note,
variable_info_note
)MS1 peak table name. https://tidymicrobiome.github.io/microbiomedataset/articles/data_import_and_export.html
Sample information name. https://tidymicrobiome.github.io/microbiomedataset/articles/data_import_and_export.html
MS1 peak table name. Columns are samples and rows are variables.
otu_tree
taxa_tree
ref_seq https://tidymicrobiome.github.io/microbiomedataset/articles/data_import_and_export.html
Sample information name. https://tidymicrobiome.github.io/microbiomedataset/articles/data_import_and_export.html
Sample information name. https://tidymicrobiome.github.io/microbiomedataset/articles/data_import_and_export.html
A microbiome_dataset-class object.
expression_data <-
as.data.frame(matrix(
sample(1:100, 100, replace = TRUE),
nrow = 10,
ncol = 10
))
rownames(expression_data) <- paste0("OTU", 1:nrow(expression_data))
colnames(expression_data) <-
paste0("Sample", 1:ncol(expression_data))
expression_data
#> Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9
#> OTU1 14 28 58 12 23 30 90 86 71
#> OTU2 69 45 11 87 68 100 65 54 37
#> OTU3 74 74 69 19 93 89 66 23 90
#> OTU4 13 48 5 68 21 6 40 14 13
#> OTU5 35 13 76 19 74 42 4 4 83
#> OTU6 32 72 72 2 17 63 80 17 71
#> OTU7 61 13 17 76 89 92 5 54 51
#> OTU8 85 67 88 62 58 76 50 32 16
#> OTU9 81 82 72 97 25 10 1 25 18
#> OTU10 38 46 23 15 44 79 90 12 13
#> Sample10
#> OTU1 58
#> OTU2 55
#> OTU3 11
#> OTU4 10
#> OTU5 92
#> OTU6 13
#> OTU7 28
#> OTU8 56
#> OTU9 95
#> OTU10 97
variable_info <-
as.data.frame(matrix(
sample(letters, 70, replace = TRUE),
nrow = nrow(expression_data),
ncol = 7
))
rownames(variable_info) <- rownames(expression_data)
colnames(variable_info) <-
c("Domain",
"Phylum",
"Class",
"Order",
"Family",
"Genus",
"Species")
variable_info$variable_id <-
rownames(expression_data)
sample_info <-
data.frame(sample_id = colnames(expression_data),
class = "Subject")
object <-
create_microbiome_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info
)
object
#> --------------------
#> microbiomedataset version: 0.99.1
#> --------------------
#> 1.expression_data:[ 10 x 10 data.frame]
#> 2.sample_info:[ 10 x 2 data.frame]
#> 3.variable_info:[ 10 x 8 data.frame]
#> 4.sample_info_note:[ 2 x 2 data.frame]
#> 5.variable_info_note:[ 8 x 2 data.frame]
#> --------------------
#> Processing information (extract_process_info())
#> create_microbiome_dataset ----------
#> Package Function.used Time
#> 1 microbiomedataset create_microbiome_dataset() 2023-04-19 17:33:11