calculate_sig_score: Calculating signature score on a gene expression dataset

In IOBR/IOBR: Immune Oncology Biological Research

Calculating signature score on a gene expression dataset

Description

Calculating signature score on a gene expression dataset

Usage

calculate_sig_score(
  pdata = NULL,
  eset,
  signature = signature_collection,
  method = "pca",
  mini_gene_count = 3,
  column_of_sample = "ID",
  print_gene_propotion = FALSE,
  adjust_eset = FALSE,
  parallel.size = 1L,
  print_filtered_signatures = FALSE,
  ...
)

Arguments

pdata	phenotype data of input sample
eset	normalized transcriptomic data: normalized (CPM, TPM, RPKM, FPKM, etc.)
signature	List of gene signatures; such as 'signature_tme', 'signature_metabolism','signature_collection', 'go_bp','kegg','hallmark'
method	he methods currently supported are 'pca', 'ssgsea', 'zscore','integration'
mini_gene_count	filter out signatures with genes less than minimal gene in expression set; default is 2 for PCA and z score function
column_of_sample	Defines in which column of the 'pdata' the identifier of the sample can be found.
print_gene_propotion	logical, print the proportion of signature genes in gene matrix
adjust_eset	default is FALSE
parallel.size	default is 1
print_filtered_signatures	logical, print filtered signatures has gene count less than minimal gene count

Value

data frame with pdata and signature scores for gene sets; signatures in columns, samples in rows

Author(s)

Dongqiang Zeng

References

1. Hänzelmann S, Castelo R, Guinney J (2013). “GSVA: gene set variation analysis for microarray and RNA-Seq data.” BMC Bioinformatics, 14, 7. doi: 10.1186/1471-2105-14-7

2. Mariathasan, S., Turley, S., Nickles, D. et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature 554, 544–548 (2018).

Examples

# Loading TCGA-STAD expresion data(raw count matrix)
data("eset_stad", package = "IOBR")
# transform count data to tpm
eset <- count2tpm(eset_stad, idType = "ensembl")
# signature score estimation using PCA, z-score, or ssgsea method
calculate_sig_score(eset = eset, signature = signature_tme, method = "pca")

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.