subjectReport,PAM50-method {pbcmc} | R Documentation

## PAM50 permutation test results reports

### Description

`subjectReport` is basically a grid.arrange object which basically consists of three main parts: a summary table, a two row ggplot2 facet_wrap with scatter ggplots (Wickham 2009) of subject expression and PAM50 centroids (Perou et al. 2000 & 2010) and a textGrob with the simulation parameter used. Particularly:

tableGrob

  with the following fields:

  $Summary

    subject name, PAM50 and Permuted subtype

  $Fields

    for the five PAM50 subtypes:

    - Correlation: PAM50 centroid correlation with observed subject exprs.

    - p-value: permutation p-value obtained using the simulation.

    - FDR: adjusted p-value using False Discovery Rate.

ggplot facet_wrap

  two rows to display scatter subject exprs vs PAM50 centroids, in addition to a the linear regression fix. If subject, has an unique subtype, then the graph is in red. In addition, if simulated permutations were run with keep=TRUE option, then null distribution boxplots are plotted with observed correlations as a big round point.

textGrob

  the permutation @parameter slot used in the simulation.

### Usage

    ## S4 method for signature 'PAM50'
    subjectReport(object, subject)

    ## S4 method for signature 'PAM50'
    databaseReport(object, fileName, ...,
        verbose = getOption("verbose", default = TRUE))

    ## S4 method for signature 'PAM50'
    summary(object, ...)

### Arguments

`object` | a PAM50 object.
`subject` | integer to select the appropriate subject to report.
`fileName` | character with the name of the pdf report file to save.
`...` | additional parameters for pdf function call.
`verbose` | should the user feedback be displayed? By default value is "verbose" global option parameter, if present, or FALSE otherwise.

### Details

`summary` it basically prints descriptive data of PAM50 dataset, the test parameters used, a frequency table of PAM50 Subtypes and a contingency table with Classes vs PAM50 Subtypes.

`databaseReport` basically is a pdf report where the first page is a global summary of the database, i.e., a `summary` contingency table of permutation test classes against original PAM50 subtypes results. The following pages are the database respective `subjectReport` outputs.

### Value

depending on function call:

`subjectReport` | a grid.arrange object.
`databaseReport` | a pdf file with database summary and `subjectReport`s.
`summary` | Console summary statistics plus a data.frame

### Author(s)

Cristobal Fresno cfresno@bdmg.com.ar, German A. Gonzalez ggonzalez@bdmg.com.ar, Andrea S. Llera allera@leloir.org.ar and Elmer Andres Fernandez efernandez@bdmg.com.ar

### References

1. Perou CM, Sorlie T, Eisen MB, et al., 2000, Molecular portraits of human breast tumors. Nature 406:747-752.

2. Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PB., 2010, Clinical implementation of the intrinsic subtypes of breast cancer, The Lancet Oncology 11(8):718-719.

3. Wickham H, ggplot2: elegant graphics for data analysis. Springer New York, 2009.

### See Also

`PAM50` for a complete example.

Other PAM50: `as`, `classify,PAM50-method`, `filtrate,PAM50-method`, `pam50centroids`, `permutate,PAM50-method`, `subtypes,PAM50-method`

Other PAM50: `as`, `classify,PAM50-method`, `filtrate,PAM50-method`, `pam50centroids`, `permutate,PAM50-method`, `subtypes,PAM50-method`

Other PAM50: `as`, `classify,PAM50-method`, `filtrate,PAM50-method`, `pam50centroids`, `permutate,PAM50-method`, `subtypes,PAM50-method`

### Examples

    ##Using pam50centroids package example data
    data(pam50centroids)
    pam50centroids

    ##This object has already run filtrate, classify and permutate. So, now
    ##we can obtain some reports:
    ##1) database summary
    summary(pam50centroids)

    ##2)Individual subject report. If keep=FALSE boxplot panel is not available
    subjectReport(pam50centroids, subject=1)##Basal subtype
    subjectReport(pam50centroids, subject=1)##Her2 subtype

    ##3) complete database report
    #databaseReport(pam50centroids, fileName="PAM50.pdf", verbose=TRUE)

[Package pbcmc version 1.8.0 Index]