e50-estimateScore: Calculation of stromal, immune, and ESTIMATE scores

In estimate: Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data

Description

This function computes stromal, immune, and ESTIMATE scores per sample using gene expression data.

Usage

estimateScore(input.ds,
              output.ds,
              platform = c("affymetrix", "agilent", "illumina"))

Arguments

input.ds	character string specifying name of input GCT file containing stromal, immune, and estimate scores for each sample
output.ds	character string specifying name of output file
platform	character string indicating platform type. Defaults to "affymetrix"

Details

This method is based on single sample gene set enrichment analysis (ssGSEA) algorithm. This function computes stromal, immune, and ESTIMATE scores using gene-level expression data. For Affymetrix platform data, tumor purity are derived from ESTIMATE scores by applying non-linear squares methods to TCGA Affymetrix expression data (n=995).

Value

Returns data.frame with components:

• StromalScorenumeric scalar specifying the presence of stromal cells in tumor tissue

• ImmuneScorenumeric scalar specifying the level of infiltrating immune cells in tumor tissue

• ESTIMATEScorenumeric scalar specifying tumor cellularity

• TumorPuritynumeric scalar specifying ESTIMATE-based tumor purity with value in range[0,1]

Author(s)

Kosuke Yoshihara [e-mail]

References

Subramanian A, et al.
"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles."
Proc Natl Acad Sci U S A 2005, 102:15545-15550.

Barbie DA, et al.
" Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1."
Nature 2009, 462:108-112.

Verhaak RG, et al.
" Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1."
Cancer Cell 2010, 17:98-110.

Carter SL, et al.
"Absolute quantification of somatic DNA alterations in human cancer."
Nat Biotechnol 2012, 30:413-421.

Examples

in.file <- system.file("extdata", "sample_input.gct", package="estimate")
out.file <- tempfile(pattern="estimate", fileext=".gct")
estimateScore(in.file, out.file)

estimate documentation built on May 2, 2019, 4:38 p.m.