View source: R/getBaselineDivergence.R
getBaselineDivergence | R Documentation |
Calculates sample dissimilarity between the given baseline and other
time points, optionally 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
.
getBaselineDivergence(
x,
group = NULL,
time_field,
name_divergence = "divergence_from_baseline",
name_timedifference = "time_from_baseline",
assay.type = "counts",
FUN = vegan::vegdist,
method = "bray",
baseline_sample = NULL,
altexp = NULL,
dimred = NULL,
n_dimred = NULL,
...
)
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 |
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 |
baseline_sample |
Optional. A character vector specifying the baseline sample(s) to be used. If the "group" argument is given, this must be a named vector; one element per group. |
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 |
The group argument allows calculating divergence per group. Otherwise, this is done across all samples at once.
The baseline sample/s always need to belong to the data object i.e. they can be merged into it before applying this function. The reason is that they need to have comparable sample data, at least some time point information for calculating time differences w.r.t. baseline sample.
The baseline time point is by default defined as the smallest time point (per group). Alternatively, the user can provide the baseline vector, or a list of baseline vectors per group (named list per group).
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)
library(dplyr)
data(hitchip1006)
tse <- mia::transformCounts(hitchip1006, method = "relabundance")
# Subset to speed up example
tse <- tse[, colData(tse)$subject %in% c("900", "934", "843", "875")]
tse2 <- getBaselineDivergence(tse,
group = "subject",
time_field = "time",
name_divergence = "divergence_from_baseline",
name_timedifference = "time_from_baseline",
assay.type="relabundance",
FUN = vegan::vegdist,
method="bray")
tse2 <- getBaselineDivergence(tse,
baseline_sample = "Sample-875",
group = "subject",
time_field = "time",
name_divergence = "divergence_from_baseline",
name_timedifference = "time_from_baseline",
assay.type="relabundance",
FUN = vegan::vegdist,
method="bray")
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