AGDEX (version 1.20.0)

get.gset.result.details: Extract gene-level details from gene-set results

Description

A function to extract the probe-sets level details for gene-set results, i.e. obtain the differential expression statistics for probe-sets assigned to the gene-sets. This allows users to explore which probe-sets results contribute the most to gene-set differential expression analysis statistics and gene-set agreement of differential expression statistics.

Usage

get.gset.result.details(agdex.result, gset.ids = NULL, alpha=0.01)

Arguments

agdex.result

agdex result returned by function agdex

gset.ids

a vector of gene-set IDs. If NULL, the result will return gene level details for all significant gene-sets at a chosen significant level alpha.

alpha

significance level of gene-set, default set to 0.01

Value

This function returns a list of three components.

gsetA.details

Gene-set details result for experiment A, including differential expression statistic and p-value for each probe-set in each gene-set. Each row represents a probe-set from A. The columns give gene-set name, enrichment statistic and its corresponding p-values, differential expression statistics and p-values

gsetB.details

similar result of gene-set details for experiment B. Rows and columns give the similar information to gsetA.details.

agdex.details

A data frame. Each row gives results for one probe-set pair. The columns give the gene-set names, cosine statistic and difference of proportions statistic and p-values, meta statistic and its p-value.

See Also

write.agdex.gset.details; read.agdex.gset.details

Examples

# Load saved result run by agdex routine               
data(agdex.res)

# obtain gene-set result
gset.res.all <- get.gset.result.details(agdex.res,gset.ids = NULL, alpha=0.01)

# obtain the detailed gene set for specified gene-sets 
gset.res0 <- get.gset.result.details(agdex.res, gset.ids=c("DNA_CATABOLIC_PROCESS","GOLGI_STACK"), alpha=0.01)