TCGAanalyze_Preprocessing: Array Array Intensity correlation (AAIC) and correlation...
In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Description
Usage
Arguments
Value
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
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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
TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.
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Description Usage Arguments Value
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
1 2 3 4 5 6 7 8 | 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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