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Assemble all bettr input into a SummarizedExperiment object

Source: R/assembleSE.R
assembleSE.Rd

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.

Usage

assembleSE(
  df,
  idCol = "Method",
  metrics = setdiff(colnames(df), idCol),
  initialWeights = NULL,
  initialTransforms = list(),
  metricInfo = NULL,
  metricColors = NULL,
  idInfo = NULL,
  idColors = NULL
)

Arguments

df

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.

idCol

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).

metrics

Character vector, indicating which of the columns of df that correspond to metrics of interest. Only metrics included here will be displayed.

initialWeights

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.

initialTransforms

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.

metricInfo

data.frame with annotations for metrics. Must have a column named 'Metric' identifying the respective metrics.

metricColors

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.

idInfo

data.frame with annotations for entities. Must have a column named according to idCol identifying the respective entities.

idColors

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.

Value

A SummarizedExperiment object with rows corresponding to methods and columns corresponding to metrics.

Author

Charlotte Soneson

Examples

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)