computeGES: Computation of gene expression signature scores.

Description Usage Arguments Details Value References Examples

View source: R/computeGES.R

Description

Computes gene expression signature scores. Also draws boxplots representing the average signature scores for each subtype.

Usage

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computeGES(expr, pred, rnaseq = FALSE)

Arguments

expr

A SummarizedExperiment object or a matrix containig gene expression profiles. If input is a SummarizedExperiment, the first element in the assays list should be a matrix of gene expression. Rows and columns of the gene expression matrix correspond to genes and samples, respectively (rownames must be to gene symbols).

pred

A vector of predicted consensus molecular subtypes.

rnaseq

logical to determine if input data is RNA-Seq gene expression profile. By default, it is FALSE.

Details

computeGES calculates the following 7 gene expression signature scores:

Value

A matrix of gene expression signature scores.

References

Aran, D. et al. (2017). xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome biology, 18, 220.

Carter, S.L. et al. (2006). A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nature genetics, 38, 1043.

Malta, T.M. et al. (2018). Machine learning identifies stemness features associated with oncogenic dedifferentiation. Cell, 173, 338-354.

Tan, T.Z. et al. (2014). Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients. EMBO molecular medicine, 6, 1279-93.

Yoshihara, K. et al. (2013). Inferring tumour purity and stromal and immune cell admixture from expression data. Nature communications, 4, 2612.

Examples

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# Load gene expression profiles of TNBC samples
data(GSE25055)

# Predict consensus molecular subtypes of TNBC samples
prediction <- predictCMS(expr = GSE25055)

# Compute gene expression signature scores
resultGES <- computeGES(expr = GSE25055, pred = prediction, rnaseq = FALSE)

TNBC.CMS documentation built on Nov. 8, 2020, 7:53 p.m.