pbcmc (version 1.0.0)

subjectReport,PAM50-method: 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

"subjectReport"(object, subject)   
"databaseReport"(object, fileName, ...,   verbose = getOption("verbose", default = TRUE))   
"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.

Value

depending on function call:

subjectReport

a grid.arrange object.

databaseReport

a pdf file with database summary and subjectReports.

summary

Console summary statistics plus a data.frame

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.

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)