loopsquaremodel: Create 'squaremodel' summaries for all samples in a...

In tgac-vumc/ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Create squaremodel summaries for all samples in a QDNAseq-object

Description

loopsquaremodel performs a squaremodel fitting on all samples in a QDNAseq-object. It prints the summaries of the squaremodels to the specified output directory. It also returns a list with squaremodels which can be saved to a variable.

Usage

loopsquaremodel(object, ptop = 5, pbottom = 1, prows = 100, 
                method = 'RMSE', penalty = 0, penploidy = 0,
                outputdir, imagetype = 'pdf', trncname = FALSE, 
                returnmodels = FALSE, printplots = TRUE, 
                printobjectsummary = TRUE)

Arguments

object	QDNAseq-object
ptop	Numeric. Sets the highest ploidy at which to start testing fits. Default = 5
pbottom	Numeric. Sets the lowest ploidy to be tested. Default = 1
prows	Integer. Sets the resolution of the ploidy-axis. Determines how many decrements are used to get from ptop to pbottom (see below). Therefore, the actual number of rows is actually prows + 1. Default = 100
method	Character string specifying which error method to use. For more documentation, consult the vignette. Can be "RMSE", "SMRE", or "MAE". Default = "RMSE"
penalty	Numeric. Penalizes fits at lower cellularities. Suggested values between 0 and 1. Default = 0 (no penalty)
penploidy	Numeric. Penalizes fits that diverge from 2N with the formula (1+abs(ploidy-2))^penploidy. Default = 0
outputdir	Character string. Print the plots to this directory
imagetype	Character string. Plots are printed to file using this graphics device. "pdf" will result in pdf-files containing 8 pages with individual plots, while the other devices print 2x4 mosaics per sample. Default = "pdf"
trncname	Logical. If set to TRUE, trncname truncates the sample name from the first instance of "_" in the name. You can also specify the regular expression here, e.g. trncname = "-.*" truncates the name from the first dash. Default = FALSE
returnmodels	Logical. Return the squaremodel results as a list. If set to TRUE, the entire squaremodel is returned for each sample. You can also specify which aspects of the model you wish to capture, for instance returnmodels = c("penalty", "minimadf"). The sample name will always be included as the first listed item. Default = FALSE
printplots	Logical. Print the plots to file. Note that the object summary is not affected by this argument. Default = TRUE
printobjectsummary	Logical. Print the object summary to file. Default = TRUE

Details

This function is basically the squaremodel equivalent of ploidyplotloop. One key difference is the output. loopsquaremodel makes a single page summary of each sample in the object. It can also return a list with the squaremodels of each sample as a variable within the R environment. The squaremodels are supplemented with the sample names. The output printed to file is optional (though by default enabled).

Value

Optionally returns a list with squaremodels (or the selected items of interest from the models) for each sample in a QDNAseq-object. If printplots is TRUE, the plots will be printed to file. If printobjectsummary is TRUE, an object summary will be printed, containing the matrixplot and the copy number plot of the best fit of each sample.

Note

In case of large numbers of samples, you may have to set printobjectsummary to FALSE to prevent file size or memory issues. For similar reasons, the default of returnmodels is FALSE.

Author(s)

Jos B. Poell

See Also

squaremodelsummary, squaremodel, ploidyplotloop

Examples

## Not run: 
  data("copyNumbersSegmented")
  loopsquaremodel(copyNumbersSegmented, penalty = 0.5, penploidy = 0.5)
  
## End(Not run)
lsm <- loopsquaremodel(copyNumbersSegmented, printplots = FALSE, 
  printobjectsummary = FALSE, penalty = 0.5, penploidy = 0.5, 
  returnmodels = TRUE)
ls(lsm[[1]])
lsm[[1]]$samplename
lsm[[1]]$matrixplot

tgac-vumc/ACE documentation built on Nov. 29, 2022, 12:15 a.m.