UniD.pred: Diagnostic Prediction

In JieYang031/UniD: Unified Diagnostic Platform for Gliomas

Description

Used to predict other genomic information, including: (1) chromosome 1p/19q co-deletion status; (2) IDH mutation status; (3) ATRX mutation status; (4) TERT promoter mutation status; (5) TCGA gene expression subtype; (6) MGMT expression level by tumor. When applying the prediction models, missing values may exist in the input data. The number of missing values will be checked. If high proportion of input data are missing values, the predicted results may have quality issues.

Usage

UniD.pred(inputdata, inputvalueType = "B", inputdata.BMIQ,
  Pred.1p19q = TRUE, Pred.IDH = TRUE, Pred.ATRX = TRUE,
  Pred.TERTp = TRUE, Pred.ExpressSubtype = TRUE, outDir, write)

Arguments

inputdata	input data with columns as samples and rows as probes, could be either Beta.raw generated from UniD.dataqc or Beta.clean generated from UniD.probefilter.
inputvalueType	indicate the inputdata value type. Can be "B" or "M". By default is Beta value "B".
inputdata.BMIQ	input data after BMIQ normalized with columns as samples and rows as probes. Must be Beta value. Suggest to be the Beta.BMIQ generated by UniD.BMIQ.
Pred.1p19q	whether perform chromosome 1p/19q co-deletion status prediction. Default is TRUE.
Pred.IDH	whether perform IDH mutation status prediction, default is TRUE.
Pred.ATRX	whehter perform ATRX mutation status prediction, default is TRUE.
Pred.TERTp	whehter perform TERT promoter mutation status prediction, default is TRUE.
Pred.ExpressSubtype	whether perform TCGA gene expression subtype prediction, including Classical/C, Mesenchymal/M, and Proneural/P. Default is TRUE.
outDir	The directory where the prediction result saved
write	wehther save the data generated within the function

Value

A data frame with predicted results, rows are samples, columns are each predicted genomic information

Examples

## Not run: 
Pred <- UniD.pred(inputdata = Beta.raw, inputvalueType = "B", inputdata.BMIQ
= Beta.BMIQ, Pred.1p19q = T, Pred.IDH = T, Pred.ATRX = T, Pred.TERTp = T,
Pred.ExpressSubtype = T, Pred.MGMTExpress = T, outDir = "~/Desktop/output/",
write = T)

## End(Not run)

JieYang031/UniD documentation built on May 5, 2021, 5:16 p.m.