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 2.10.5 Index]