View source: R/microbiome_functions.R
physeq.create | R Documentation |
Function to create phyloseq obejct, with additional quality control measures to ensure input dataframes are correctly aligned for phyloseq.
physeq.create( asvdf, taxdf, mapdf, ID.col, export.asvsp = TRUE, export.wd = getwd() )
asvdf |
Dataframe containing ASV sequence count data for each sample. Rows are sequences and column are samples. Rownames must be set to sequence ID.. |
taxdf |
Dataframe contaningg taxonomic classification of each ASV. Rows are sequences and columns are samples. Rownames must be set to sequence ID. |
mapdf |
Dataframe containing sample meta data (e.g clinical variables). Rows are samples and columns are metadata variables (e.g age, sex, clinical variables, etc.) |
ID.col |
#String. Name of the column in mapdf that contains sample IDs. (E.g |
export.asvsp |
# |
export.wd |
#Directory path as a string (e.g |
Phyloseq object.
dat <- physeq.create(asvdf = asv, taxdf = taxanomy, mapdf = metadata, ID.col = "sample_ID", export.asvsp = FALSE)
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