TCGAanalyze_Preprocessing: Array Array Intensity correlation (AAIC) and correlation...

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier

Description

TCGAanalyze_Preprocessing perform Array Array Intensity correlation (AAIC). It defines a square symmetric matrix of spearman correlation among samples. According this matrix and boxplot of correlation samples by samples it is possible to find samples with low correlation that can be identified as possible outliers.

Usage

TCGAanalyze_Preprocessing(
  object,
  cor.cut = 0,
  datatype = names(assays(object))[1],
  filename = NULL,
  width = 1000,
  height = 1000
)

Arguments

object	gene expression of class RangedSummarizedExperiment from TCGAprepare
cor.cut	is a threshold to filter samples according their spearman correlation in samples by samples. default cor.cut is 0
datatype	is a string from RangedSummarizedExperiment assay
filename	Filename of the image file
width	Image width
height	Image height

Value

Plot with array array intensity correlation and boxplot of correlation samples by samples

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.