classify_gsva_abs: Classification Using Absolute GSVA Score Thresholds

In a-thind/PathAnalyser: ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets

Classification Using Absolute GSVA Score Thresholds

Description

Classifies samples according to pathway activity by first ranking samples by their GSVA score and assessing evidence of expression consistency of each sample with the up-regulated gene-set and down-regulated gene-set of the gene signature using absolute GSVA score thresholds. GSVA scores generated by the GSVA algorithm provide a measure of expression abundance of the up-regulated and down-regulated gene-sets, which PathAnalyser uses to assess expression consistency with both parts (up-regulated and down-regulated gene-sets) of the gene signature using the user-supplied absolute GSVA score thresholds as thresholds for expression consistency with each part of the signature.

Usage

classify_gsva_abs(
  expr_mat,
  sig_df,
  up_thresh.low,
  up_thresh.high,
  dn_thresh.low,
  dn_thresh.high
)

Arguments

expr_mat	Normalised expression data set matrix comprising the expression levels of genes (rows) for each sample (columns) in a data set. Row names are gene symbols and column names are sample IDs / names. Gene expression matrices can contain normalised (logCPM transformed) RNASeq or microarray transcriptomic data.
sig_df	Gene expression signature for a specific pathway given as data frame with the first column named "gene" containing a list of genes that are the most differentially expressed when the given pathway is active and the second column named "expression" containing their corresponding expression: -1 for down-regulated genes and 1 for up-regulated genes.
up_thresh.low	Number denoting the absolute GSVA score threshold for categorizing a sample as having inconsistent expression with the up-regulated gene-set from the gene signature.
up_thresh.high	Number denoting the absolute GSVA score threshold for categorizing a sample as having consistent expression with the up-regulated gene set from the gene signature.
dn_thresh.low	Number denoting the absolute GSVA score threshold for categorizing a sample as having consistent expression with the down-regulated gene-set from the gene signature.
dn_thresh.high	Number denoting the absolute GSVA score threshold for categorizing a sample as having inconsistent expression with the down-regulated gene-set from the gene signature.

Details

Four thresholds are specified by the user:

1. "up_thresh.low" - a GSVA score threshold for considering a sample as having inconsistent expression with up-regulated gene-set.

2. "up_thresh.high" - a GSVA score threshold for considering a sample as having expression consistent with the up-regulated gene-set up-regulated gene set

3. "dn_thresh.low" - a GSVA score threshold for considering a sample as having consistent expression with down-regulated gene-set

4. "dn_thresh.high" - a GSVA score threshold for considering a sample as having inconsistent expression with the down-regulated gene-set. Samples that have consistent expression with both the up-regulated and down-regulated gene-sets of the signature are classified as "Active", those with inconsistent expression with both parts of the signature are classified as "Inactive" and the rest of the samples are classified as "Uncertain".

Value

A data frame containing a list of samples as the first column and their classified pathway activity (Active, Inactive or Uncertain) in the second column.

Author(s)

Anisha Thind [e-mail]

Examples

# Default thresholds for up-regulated and down-regulated gene-sets
## Not run: classes_df <- classify_gsva_abs(ER_dataset, ER_sig, up_thresh.low=-0.25,
     up_thresh.high=0.25, dn_thresh.low=-0.25, dn_thresh.high=0.35)
## End(Not run)

a-thind/PathAnalyser documentation built on May 6, 2022, 9:50 a.m.