get.gset.result.details {AGDEX} | R Documentation |
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.
get.gset.result.details(agdex.result, gset.ids = NULL, alpha=0.01)
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 |
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. |
Stan Pounds <stanley.pounds@stjude.org; Cuilan Lani Gao <cuilan.gao@stjude.org>
write.agdex.gset.details
; read.agdex.gset.details
# 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)