UniD: UniD: A package for unified diagnostic platform for gliomas.
In JieYang031/UniD: Unified Diagnostic Platform for Gliomas

Description Usage Arguments Details Value Functions See Also Examples

View source: R/UniD.R

The UniD package use the DNA methylation microarray data to predict other genomic information, including IDH mutation, ATRX mutation, TERT promoter mutation, chromosome 1p/19q co-deletion, TCGA gene expression subtypes ( Classical, Mesenchymal, and Proneural) with their probability, and MGMT gene expression level.

1	UniD(dataDir, outDir, arrayType, sampleType, write)

`dataDir`	directory where raw data stored
`outDir`	directory where output data should be saved if write = T
`arrayType`	the platform which raw data generated, can be "450k" or "EPIC"
`sampleType`	Indicate the input data are "FFPE" or "other"
`write`	whether the output should be saved, highly recommended

UniD package providing two categories of functions:

(1) Data processing and quality control:

UniD.intctl, UniD.dataqc, UniD.probefilter

(2) Genomic information prediction:

UniD.pred

A data frame with all predicted results

UniD.load: load the raw data

UniD.intctl: check the internal control probes which can reflect different aspects of experiments quality.

UniD.dataqc: check data quality in three aspects: detection P-value, beadcount per probes, and missing values.

UniD.probefilter: filter out probes belong to different categories which may have quality issues, and probes with high proportion of missing values.

UniD.BMIQ: normalize type I and type II probes based on BMIQ method.

UniD.pred: predict othergenomic information using Illumina DNA methylation microarray data, currently support 450k and EPIC platform

The BMIQ normalization method is adapted from BMIQ.

## Not run: 
 pred.result <- UniD(dataDir = "~/Desktop/input/", outDir = "~/Desktop/output/",
 arrayType = "450k", sampleType = "other", write = T)

## End(Not run)