metrics: Quality control metrics

Description Usage Arguments Details Value Functions Note Author(s) Examples

Description

Quality control metrics

Usage

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metrics(object, ...)

metricsPerSample(object, ...)

## S4 method for signature 'SummarizedExperiment'
metrics(object, return = c("tbl_df", "DataFrame"))

## S4 method for signature 'SingleCellExperiment'
metrics(object, return = c("tbl_df", "DataFrame"))

## S4 method for signature 'SingleCellExperiment'
metricsPerSample(
  object,
  fun = c("mean", "median", "sum"),
  return = c("tbl_df", "DataFrame")
)

Arguments

object

Object.

return

character(1). Return type. Uses match.arg() internally and defaults to the first argument in the character vector.

fun

character(1). Mathematical function name to apply. Uses match.arg() internally.

...

Additional arguments.

Details

metrics() takes data stored in colData() and consistently returns a tbl_df or DataFrame with sampleName and interestingGroups columns, even when these columns are not defined in colData(). This is designed to integrate with plotting functions that use ggplot2 internally.

Value

Object of class determined by return argument.

Functions

Note

These functions will error intentionally if no numeric columns are defined in colData().

Updated 2019-08-18.

Author(s)

Michael Steinbaugh, Rory Kirchner

Examples

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data(
    RangedSummarizedExperiment,
    SingleCellExperiment,
    package = "acidtest"
)

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
object <- calculateMetrics(object)
x <- metrics(object)
print(x)

## SingleCellExperiment ====
object <- SingleCellExperiment
object <- calculateMetrics(object)
x <- metrics(object)
print(x)
x <- metricsPerSample(object, fun = "mean")
print(x)

acidgenomics/basejump documentation built on Nov. 21, 2019, 1:36 a.m.