Assemble all bettr input into a SummarizedExperiment
object. This
has the advantage of keeping all data together in a single object, and can
be used as input to bettr
or bettrGetReady
, instead of
providing the individual components.
A data.frame
in wide format. Should contain one column
with the IDs of the entities to be compared, and one column for each
metric to use for the comparison.
Character scalar, indicating the name of the column of df
and/or idInfo
that contains IDs of the entities to be compared
(e.g., methods).
Character vector, indicating which of the
columns of df
that correspond to metrics of interest. Only metrics
included here will be displayed.
Named numeric vector providing initial weights for
each metric to use for aggregating them into a final score. Must contain
one entry per metric included in metrics
.
Named list with initial values of transformation parameters for each metric. Each list entry should correspond to one metric, and take the form of a list with up to four elements, named:
* **flip**: Logical scalar; whether or not to flip the sign of the
metric values. Defaults to `FALSE`.
* **offset**: Numeric scalar; offset to add to the (flipped)
metric values. Defaults to `0`.
* **transform**: Character scalar; one of 'None', 'z-score',
'\[0,1\]', '\[-1,1\]', 'Rank', 'Rank+\[0,1\]' or 'z-score+\[0,1\]',
indicating which transform to apply to
the metric values (after any flipping and/or adding the offset).
Defaults to 'None'.
* **cuts**: Numeric vector or `NULL`; the cut points that will
be used to bin the metric values (after the other transformations).
Defaults to `NULL`.
Only values deviating from the defaults need to be explicitly specified,
the others will be initialized to their default values.
data.frame
with annotations for metrics. Must have
a column named 'Metric' identifying the respective metrics.
Named list with colors used for columns of
metricInfo
. Should follow the format required for ComplexHeatmap
heatmap annotations. The list can include an entry named 'Metric', which
contains a named vector with colors to use for metrics.
data.frame
with annotations for entities. Must have a
column named according to idCol
identifying the respective entities.
Named list with colors used for columns of idInfo
.
Should follow the format required for ComplexHeatmap heatmap
annotations. The list can include an entry named according to idCol
,
which contains a named vector with colors to use for entities.
A SummarizedExperiment object with rows corresponding to methods and columns corresponding to metrics.
df <- data.frame(Method = c("M1", "M2", "M3"),
metric1 = c(1, 2, 3),
metric2 = c(3, 1, 2))
metricInfo <- data.frame(Metric = c("metric1", "metric2", "metric3"),
Group = c("G1", "G2", "G2"))
idInfo <- data.frame(Method = c("M1", "M2", "M3"),
Type = c("T1", "T1", "T2"))
bettrSE <- assembleSE(df = df, metricInfo = metricInfo, idInfo = idInfo)