createPRPS: Generate PRPS for RUV-III

In AbhishekSinha28/tgcapkg: TGCA Data Analysis

Generate PRPS for RUV-III

Description

This function is a part of the data analysis functionality of tcgaCleaneR. It creates pseudo-replicates of pseudo-samples (PRPS) for unwanted variations like Library size, Batches and Purity in TCGA Pan Cancer Datasets with Cancer biology like Breast Cancer data (BRCA), Lung Cancer (LUAD), Colon Cancer (COAD) and Rectum Cancer (READ). In the function batch refers to the source of Batch Effect variation like Time and Plate which captures variation across biology while factors like Purity captures variation within biology.

Usage

createPRPS(
  expr.data,
  sample.info,
  librarySize,
  batch,
  biology,
  purity,
  include.ls,
  include.purity,
  minSamplesPerBatchPS,
  minSamplesForPuirtyPS,
  minSamplesForPurityPerBiology,
  minSamplesForLibrarySizePerBatch,
  minSamplesForLibrarySizePS
)

Arguments

expr.data	S4 data object: Cancer Gene expression data
sample.info	S4 data object: Cancer data Sample information
librarySize	character: Library Size variable in input sample.info data object.
batch	character: Batch effect factors. In current package version batch can take values like 'Year', 'Plate' or both
biology	character: Biology of cancer type. TCGA datasets have biology for only four Cancer types i.e. Lung (LUAD), Breast (BRCA), Rectum (READ) & Colon (COAD). So the function supports only these four datasets for RUV-III and PRPS analysis. Default is 'Subtypes'.
purity	character: Purity variable in input data object
include.ls	logical: Do we need to consider library size in creating pseudo samples
include.purity	logical: Do we need to consider purity in creating pseudo samples
minSamplesPerBatchPS	numeric: Minimum number of samples per batch for creating Pseudo Samples
minSamplesForPuirtyPS	numeric: Minimum number of samples for creating Pseudo Samples for purity.
minSamplesForPurityPerBiology	numeric: Number of samples for purity per biology for creating Pseudo Samples
minSamplesForLibrarySizePerBatch	numeric: Number of samples for library size per batch for creating Pseudo Samples
minSamplesForLibrarySizePS	numeric: Minimum number of samples for creating Pseudo Samples for library size

Value

A S4 list object with the Pseudo replicate for pseudo samples for different batches, library size and purity.

Examples

## Not run: 
createPRPS(expr.data, sample.info, librarySize = 'ls', batch=c('Year', 'Plates'), biology = 'Subtypes',
purity='Purity_singscore',include.ls=TRUE, include.purity=TRUE,
minSamplesPerBatchPS = 3, minSamplesForPuirtyPS = 3, minSamplesForPurityPerBiology = 12,
minSamplesForLibrarySizePerBatch = 6,minSamplesForLibrarySizePS = 3)

## End(Not run)

AbhishekSinha28/tgcapkg documentation built on May 3, 2022, 7:40 a.m.