plotRankedFeature {BioMM} | R Documentation

## Plot top outcome-associated features

### Description

Plot top ranked outcome-associated features from stage-2 data. The ranking criteria are based on metrics such as Nagelkerke pseudo R-square.

### Usage

    plotRankedFeature(
      data,
      posF = TRUE,
      topF = 10,
      blocklist,
      binarize = FALSE,
      rankMetric = c("AUC", "R2", "Zscore", "negPlogit", "negPwilcox", "size"),
      colorMetric = c("AUC", "R2", "Zscore", "negPlogit", "negPwilcox", "size"),
      core = MulticoreParam(),
      pathTitle = "GO pathways",
      fileName = NULL
    )

### Arguments

`data` | The input stage-2 data (either data.frame or matrix). Rows are the samples, columns are pathway names, except that the first column is the label (the outcome).
`posF` | A logical value indicating if only positively outcome-associated features should be used. (Default: TRUE)
`topF` | The top ranked number of features at stage-2 (`topF` >= 2). (Default: 10)
`blocklist` | A list of matrices with block IDs as the associated list member names. The block IDs identical to the stage-2 feature names. For each matrix, rows are the samples and columns are the probe names, except that the first column is named 'label'. See also `omics2pathlist`.
`binarize` | A logical value indicating if the individual features under investigation should be binarized. The default is FALSE, which provides the estimated class probabilities for each pathway-level feature. If TRUE, then the binary output is given for each feature.
`rankMetric` | A string representing the metrics used for ranking. Valid options are c("AUC", "R2", "Zscore", "negPlogit", "negPwilcox"). "negPlogit" denotes the negative log P value from the logistic regression and "negPwilcox" means the negative log P value based on the Wilcoxon test. "size" is the block size.
`colorMetric` | A string representing the metric used to color the plot. Valid options are c("AUC", "R2", "Zscore", "negPlogit", "negPwilcox"). "negPlogit" denotes the negative log P value from the logistic regression and "negPwilcox" means the negative log P value based on wilcoxon test. "size" is the block size.
`core` | The number of cores used for computation. (Default: 10)
`pathTitle` | A string indicating the name of pathway under investigation.
`fileName` | The plot file name. (Default: 'plottopF.png')

### Details

If the argument `posF` is TRUE, and no positively outcome-associated features are present in stage-2 data , then an error is reported. In addition, if `topF` is bigger than the number of positively outcome-associated features, an error is returned.

### Value

An output image file and the summary statistics of the top pathways.

### References

Perlich, C., & Swirszcz, G. (2011). On cross-validation and stacking: Building seemingly predictive models on random data. ACM SIGKDD Explorations Newsletter, 12(2), 11-15.

### See Also

`omics2pathlist`.

[Package BioMM version 1.10.0 Index]