InfiniumPurifyR: Estimate tumor enrichment using the InfiniumPurify method in...
In metamaden/InfiniumPurifyr:

Usage Arguments Value Author(s) References

View source: R/InfiniumPurifyR.R

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InfiniumPurifyR(df,calcPurity=TRUE,returnDMPonly=FALSE,plotunimod=FALSE,hyper=NULL,hypo=NULL,
                            getDMPs=FALSE,dmpVariablename=NULL, dmpVariancefiltTissue=NULL,
                            nsigprobes=NULL,varfilt=NULL,plotunimod.main=NULL,plotunimod.ymax=NULL)

`df`	Beta-value matrix (rows=markers,cols=samples) or minfi experiment summary object.
`calcPurity`	Should a purity estimate be returned? Requires hyper and hypo cpgs be specified.
`returnDMPonly`	Should differentially methylated and variable CpG probe list be returned? If TRUE, then no purity is calculated or unimodal plots generated.
`plotunimod`	Should a plot of overlayed sample densities of the probe Beta-values (with hypomethylated probes transformed to be 1 - Beta-val.) be returned? Requires hyper- and hypo-methylated probes be provided.
`hyper`	List of CpG probe IDs that are hypermethylated in tumor compared to normal samples (Beta-values remain untransformed for purity est.)
`hypo`	List of CpG probe IDs that are hypomethylated in tumor compared to normal samples (Beta-values are transformed as 1 - Beta-val.).
`getDMPs`	Whether to calculate differentially methylated and variable CpG markers. Requires dmpVariablename and dmpVariancefiltTissue be provided.
`dmpVariablename`	The character name of the variable containing tissue types to be used in calculated differential methylation. This should be accessable as in a minfi experiment summary object (eg. using 'objectname'$'dmpVariablename' or pData('objectname')$'dmpVariablename').
`dmpVariancefiltTissue`	Name of tissue type (in variable labeled as 'dmpVariablename') to be used as the reference for hypervariability when filtering DMPs.
`nsigprobes`	How many DMPs should be returned after filtering?
`varfilt`	What threshold for variance should be used to filter DMPs? Defaults to the top quantile of variant CpGs in the reference tissue ('dmpVariancefiltTissue').
`plotunimod.main`	Main title for the plot of density overlays, if plotunimod=TRUE.
`plotunimod.ymax`	Maximum y-axis value for the plot of density overlays, if plotunimod=TRUE.

List of objects as specified.

`DMPs`	Differentially methylated and variant CpGs.
`IPR estimates`	Purity estimates from hyper/hypo CpGs.
`Plot`	Overlay density plot of Beta-values/1 - Beta-values at DMPs.