getRefLimma: provide access to a limma analysis of RNA-seq profiles for...
In vjcitn/ivygapSE: A SummarizedExperiment for Ivy-GAP data
getRefLimma R Documentation
provide access to a limma analysis of RNA-seq profiles for reference histology samples
Description
provide access to a limma analysis of RNA-seq profiles for reference histology samples
Usage
getRefLimma(cache = BiocFileCache::BiocFileCache())
Value
an instance of MArrayLM-class representing regularized gene-wise ANOVAs
Note
Uses BiocFileCache::bfcadd to acquire RDS of the output
of eBayes from a public S3 bucket. The limma model
was fit using duplicateCorrelation to address multiplicity
of contributions per donor. Comparisons are to samples labeled CT-reference (cellular tumor, reference contributions),
with coefficients 2-5 corresponding to CT-mvp (microvascular proliferation),
CT-pan (pseudopalisading cells around necrosis), IT (infiltrating tumor),
and LE (leading edge), respectively.
Examples
requireNamespace("limma")
ebout = getRefLimma() # is result of eBayes
colnames(ebout$coef)
limma::topTable(ebout,2)
vjcitn/ivygapSE documentation built on May 6, 2022, 5:50 a.m.
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| getRefLimma | R Documentation |
provide access to a limma analysis of RNA-seq profiles for reference histology samples
Description
provide access to a limma analysis of RNA-seq profiles for reference histology samples
Usage
getRefLimma(cache = BiocFileCache::BiocFileCache())
Value
an instance of MArrayLM-class representing regularized gene-wise ANOVAs
Note
Uses BiocFileCache::bfcadd to acquire RDS of the output
of eBayes from a public S3 bucket. The limma model
was fit using duplicateCorrelation to address multiplicity
of contributions per donor. Comparisons are to samples labeled CT-reference (cellular tumor, reference contributions),
with coefficients 2-5 corresponding to CT-mvp (microvascular proliferation),
CT-pan (pseudopalisading cells around necrosis), IT (infiltrating tumor),
and LE (leading edge), respectively.
Examples
requireNamespace("limma")
ebout = getRefLimma() # is result of eBayes
colnames(ebout$coef)
limma::topTable(ebout,2)
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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