View source: R/getStepwiseDivergence.R
getStepwiseDivergence | R Documentation |
Calculates sample dissimilarity between consecutive time points (t, t+i),
within a group (subject, reaction chamber, or similar). The corresponding
time difference is returned as well. The method operates on
SummarizedExperiment
objects, and the results are stored in colData
.
getStepwiseDivergence(
x,
group = NULL,
time_field,
time_interval = 1,
name_divergence = "time_divergence",
name_timedifference = "time_difference",
assay.type = "counts",
FUN = vegan::vegdist,
method = "bray",
altexp = NULL,
dimred = NULL,
n_dimred = NULL,
...
)
getTimeDivergence(x, ...)
## S4 method for signature 'ANY'
getTimeDivergence(x, ...)
x |
A
|
group |
optional; a single character value for specifying the grouping
factor (name of a |
time_field |
a single character value, specifying the name of the
time series field in |
time_interval |
integer value indicating the increment between time steps (default: 1). If you need to take every second, every third, or so, time step only, then increase this accordingly. |
name_divergence |
a column vector showing beta diversity between samples
(default: |
name_timedifference |
field name for adding the time difference between
samples used to calculate beta diversity
(default: |
assay.type |
character indicating which assay values are used in
the dissimilarity estimation (default: |
FUN |
a |
method |
a method that is used to calculate the distance. Method is
passed to the function that is specified by |
altexp |
String or integer scalar specifying the alternative experiment containing the input data. |
dimred |
A string or integer scalar indicating the reduced dimension
result in |
n_dimred |
Integer scalar or vector specifying the dimensions to use if
|
... |
Arguments to be passed |
a
SummarizedExperiment
or
TreeSummarizedExperiment
containing the sample dissimilarity and corresponding time difference between
samples (across n time steps), within each level of the grouping factor.
#library(miaTime)
library(TreeSummarizedExperiment)
data(hitchip1006)
tse <- mia::transformCounts(hitchip1006, method = "relabundance")
# Subset to speed up example
tse <- tse[, colData(tse)$subject %in% c("900", "934", "843", "875")]
# Using vegdist for divergence calculation, one can pass
# the dissimilarity method from the vegan::vegdist options
# via the "method" argument
tse2 <- getStepwiseDivergence(tse, group = "subject",
time_interval = 1,
time_field = "time",
assay.type="relabundance",
FUN = vegan::vegdist,
method="bray")
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