runGSVA: Run gene set variation analysis

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

Use gene set variation analysis to calculate enrichment score of each sample in each subtype based on given gene set list of interest.

Usage

runGSVA(
  moic.res = NULL,
  norm.expr = NULL,
  gset.gmt.path = NULL,
  gsva.method = "gsva",
  centerFlag = TRUE,
  scaleFlag = TRUE,
  halfwidth = 1,
  annCol = NULL,
  annColors = NULL,
  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
    "#023E8A", "#9D4EDD"),
  distance = "euclidean",
  linkage = "ward.D",
  show_rownames = TRUE,
  show_colnames = FALSE,
  color = c("#366A9B", "#4E98DE", "#DDDDDD", "#FBCFA7", "#F79C4A"),
  fig.path = getwd(),
  fig.name = NULL,
  width = 8,
  height = 8,
  ...
)

Arguments

moic.res	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
norm.expr	A matrix of normalized expression data with rows for genes and columns for samples; FPKM or TPM without log2 transformation is recommended.
gset.gmt.path	A string value to indicate ABSOULUTE PATH/NAME of gene sets of interest stored as GMT format https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29.
centerFlag	A logical vector to indicate if enrichment scores should be centered; TRUE by default.
scaleFlag	A logical vector to indicate if enrichment scores should be scaled; TRUE by default.
halfwidth	A numeric value to assign marginal cutoff for truncating enrichment scores; 1 by default.
annCol	A data.frame storing annotation information for samples.
annColors	A list of string vectors for colors matched with annCol.
clust.col	A string vector storing colors for annotating each subtype at the top of heatmap.
distance	A string value of distance measurement for hierarchical clustering; 'euclidean' by default.
linkage	A string value of clustering method for hierarchical clustering; 'ward.D' by default.
show_rownames	A logic value to indicate if showing rownames (feature names) in heatmap; TRUE by default.
show_colnames	A logic value to indicate if showing colnames (sample ID) in heatmap; FALSE by default.
color	A string vector storing colors for heatmap.
fig.path	A string value to indicate the output path for storing the enrichment heatmap.
fig.name	A string value to indicate the name of the enrichment heatmap.
width	A numeric value to indicate the width of output figure.
height	A numeric value to indicate the height of output figure.
...	Additional parameters pass to pheatmap.

Value

A figure of enrichment heatmap (.pdf) and a list with the following components:

gset.list a list storing gene sets information converted from GMT format by read.gmt.

raw.es a data.frame storing raw enrichment score based on given gene sets of interest by using specified gsva.method.

scaled.es a data.frame storing z-scored enrichment score based on given gene sets of interest by using specified gsva.method.

References

Barbie, D.A. et al. (2009). Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature, 462(5):108-112.

Hänzelmann, S., Castelo, R. and Guinney, J. (2013). GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14(1):7.

Lee, E. et al. (2008). Inferring pathway activity toward precise disease classification. PLoS Comp Biol, 4(11):e1000217.

Tomfohr, J. et al. (2005). Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics, 6(1):1-11.

Yu G, Wang L, Han Y, He Q (2012). clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS, 16(5):284-287.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.