TCGAanalyze_Preprocessing {TCGAbiolinks}R Documentation

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,
  filename = NULL,
  width = 1000,
  height = 1000,
  datatype = names(assays(object))[1]
)

Arguments

object

of 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

filename

Filename of the image file

width

Image width

height

Image height

datatype

is a string from RangedSummarizedExperiment assay

Value

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


[Package TCGAbiolinks version 2.22.2 Index]