summary.goglm: Summerize GOglm Results

Description Usage Arguments Value Author(s) See Also Examples

View source: R/summary.goglm.R

Description

Summerize GOglm results (from the goglm function)

Usage

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  ## S3 method for class 'goglm'
 summary(x, en.cut = 0.05, ...)

Arguments

x

An object of class goglm

en.cut

P-value cut-off for declaring enriched categories (default = 0.05)

...

Other parameters (for future use)

Value

Some descriptive summaries based on the goglm result

Author(s)

Gu Mi mig@stat.oregonstate.edu, Yanming Di diy@stat.oregonstate.edu

See Also

summary.prepGOglm, summary

Examples

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## Load the datasets into R session:
data(ProsCan_DE)
DE_data <- ProsCan_DE
data(ProsCan_Length)
Length_data <- ProsCan_Length

## Prepare a data frame to be passed to goglm():
gene_table <- prepare(DE_data, Length_data, trans.p = "d.log", trans.l = TRUE)

## For illustration, only consider a subset of genes:
gene_data <- gene_table[1:100,1:2]

## Prepare the "category-to-genes" list:
library(goseq)
gene2cats <- getgo(rownames(gene_data), "hg18", "ensGene")
cat2genes <- revMap(gene2cats)

## Run goglm():
res <- goglm(gene_data, cat2genes, n=5)
names(res)  # "GOID"   "over.p" "anno"   "rank"

## For a summary of the GOglm results:
summary(res)

gu-mi/GOglm documentation built on May 14, 2019, 7:42 a.m.