gsea_regulon: This function performs GSEA for the negative and positive...

Description Usage Arguments Value

View source: R/GSEA_Subramanian.R

Description

This function performs GSEA for the negative and positive targets, respectively, of a regulatory gene.

Usage

1
2
3
4
5
6
gsea_regulon(
  signature,
  regulon,
  sorting = c("decreasing", "increasing"),
  weight = 1
)

Arguments

signature

Named vector of gene-level statistics (preferably t-statistics)

regulon

list object as returned by aracne2regulon (viper package)

tfmode

named numeric vector of the mode of regulation (MOR) values

likelihood

numeric vector of interaction confidence values (based on mutual information)

sorting

character indicating how to sort the signature (default is decreasing). Passed to gsea1T.

w

weight for each gene-level statistic (default = 1)

Value

a list object containing for each gene set:

signature

input signature

ES_pos

enrichment score positive targets

ES_neg

enrichment score negative targets

ES_pos_idx

enrichment score positive targets index

ES_neg_idx

enrichment score negative targets index

RS_pos

running sum for positive targets

RS_neg

running sum for negative targets

gs_idx_pos

indices of the positive targets in the signature

gs_idx_neg

indices of the negative targets in the signature

ledge_pos

gene identifiers of the leading edge for the positive targets

ledge_neg

gene identifiers of the leading edge for the negative targets

ledge_idx_pos

indices of the leading edge gene set members - positive targets

ledge_idx_neg

indices of the leading edge gene set members - negative targets


fossbert/binilib documentation built on April 23, 2021, 10:31 p.m.