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,
  stratify = c("gene", "pathway", "chromosome"), rankMetric = c("cor",
  "AUC", "ACC", "R2", "size"), colorMetric = c("cor", "AUC", "ACC", "R2",
  "size"), core = MulticoreParam(), fileName = NULL)

Arguments

data

The input stage-2 data (either data.frame or matrix). Rows are the samples, columns are gene IDs, or pathway names or chromosome IDs, 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. The block can be gene, pathway or chromosome. For each matrix, rows are the samples and columns are the probe names, except that the first column is named 'label'. See also omics2genelist; omics2pathlist; omics2chrlist

stratify

A string. The applied stratification method to generate blocklist. Valid options are c('gene', 'pathway', 'chromosome').

rankMetric

A string representing the metrics used for ranking. Valid options are c('cor', 'AUC', 'ACC', 'R2', 'size'). 'size' is the block size.

colorMetric

A string representing the metric used to color the plot. Valid options are c('cor', 'AUC', 'ACC', 'R2', 'size'). 'size' is the block size.

core

The number of cores used for computation. (Default: 10)

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.

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

omics2genelist; omics2pathlist; omics2chrlist


[Package BioMM version 1.0.0 Index]