plotROC: ROCR functions for 'Modifier' and 'ModifierSet' objects

In FelixErnst/RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

ROCR functions for Modifier and ModifierSet objects

Description

plotROC streamlines labeling, prediction, performance and plotting functions to test the peformance of a Modifier object and the data analyzed via the functionallity from the ROCR package.

The data from x will be labeled as positive using the coord arguments. The other arguments will be passed on to the specific ROCR functions.

By default the prediction.args include three values:

• measure = "tpr"

• x.measure = "fpr"

• score = mainScore(x)

The remaining arguments are not predefined.

Usage

plotROC(x, coord, ...)

## S4 method for signature 'Modifier'
plotROC(
  x,
  coord,
  score = NULL,
  prediction.args = list(),
  performance.args = list(),
  plot.args = list()
)

## S4 method for signature 'ModifierSet'
plotROC(
  x,
  coord,
  score = NULL,
  prediction.args = list(),
  performance.args = list(),
  plot.args = list()
)

Arguments

x	a Modifier or a ModifierSet object
coord	coordinates of position to label as positive. Either a GRanges or a GRangesList object. For both types the Parent column is expected to match the gene or transcript name.
...	additional arguments
score	the score identifier to subset to, if multiple scores are available.
prediction.args	arguments which will be used for calling prediction form the ROCR package
performance.args	arguments which will be used for calling performance form the ROCR package
plot.args	arguments which will be used for calling plot on the performance object of the ROCR package. If multiple scores are plotted (for example if the score argument is not explicitly set) add = FALSE will be set.

Value

a plot send to the active graphic device

References

Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer (2005): "ROCR: visualizing classifier performance in R." Bioinformatics 21(20):3940-3941 DOI: 10.1093/bioinformatics/bti623

Examples

data(msi,package="RNAmodR")
# constructing a GRanges obejct to mark positive positions
mod <- modifications(msi)
coord <- unique(unlist(mod))
coord$score <- NULL
coord$sd <- NULL
# plotting a TPR vs. FPR plot per ModInosine object
plotROC(msi[[1]],coord)
# plotting a TPR vs. FPR plot per ModSetInosine object
plotROC(msi,coord)

FelixErnst/RNAmodR documentation built on March 27, 2024, 2:42 a.m.