format_tempted {tempted} | R Documentation |
This function applies a variety of transformations to the read counts and
format the sample by feature table and meta data into a data list
that can be used as the input of tempted
and svd_centralize
.
For data that are not read counts, or data that are not microbiome data,
the user can apply their desired transformation to the data before formatting into list.
format_tempted(
featuretable,
timepoint,
subjectID,
threshold = 0.95,
pseudo = NULL,
transform = "clr"
)
featuretable |
A sample by feature matrix. |
timepoint |
The time stamp of each sample, matched with the rows of |
subjectID |
The subject ID of each sample, matched with the rows of |
threshold |
A threshold for feature filtering for microbiome data. Features with zero value percentage > threshold will be excluded. Default is 0.95. |
pseudo |
A small number to add to all the counts before
normalizing into proportions and log transformation.
Default is 1/2 of the smallest non-zero value that is specific for each sample.
This pseudo count is added for |
transform |
The transformation applied to the data.
|
A length n list of matrices as the input of tempted
and svd_centralize
. Each matrix represents a subject, with columns representing samples from this subject, the first row representing the sampling time points, and the following rows representing the feature values.
Examples can be found in tempted
.