Reads an abundance matrix into a Dataset object
read.am(file, format = "am", taxonomy = FALSE, simplify = FALSE)
| file | File path of the abundance matrix. |
|---|---|
| format | Format of the abundance table file. Either "am" or "qiime", see description for details. |
| taxonomy | Indicates whether a taxonomy assignment column is present in the abundance matrix. If FALSE, no taxonomy is expected, if a string or integer are passed, then the column with the corresponding name or number is expected to have taxonomy information. |
| simplify | Logical, indicating whether the abundance table should be coerced to a numerical matrix |
If simplify = FALSE, it returns a Dataset object, where the value of the Tax element is determined by the taxonomy argiment.
If simplify = TRUE, it returns a numeric abundance matrix. Any taxonomic information is lost in this case.
This function is a wrapper for read.table(), and reads tab-delimited text files that contain abundance matrices. It supports two formats: 1) am, this format contains a first row of sample IDs and and a first colum of taxon IDs; and 2) qiime, this format is the original QIIME format, where the first line contains a version identification string, the second row sample IDs and the first column (after second row) taxon IDs. The first two lines start witht he '#' character.