GOsummaries (version 2.6.0)

add_expression.gosummaries: Add expression data to gosummaries object

Description

Function to add expression data and its annotations to a gosummaries object.

Usage

add_expression.gosummaries(gosummaries, exp, annotation = NULL)

Arguments

gosummaries

a gosummaries object

exp

an expression matrix, with row names corresponding to the names in the Gene_lists slot

annotation

a data.frame describing the samples, its row names should match with column names of exp

Details

The data is added to the object in a "long" format so it would be directly usable by the ggplot2 based panel drawing functions panel_boxplot etc. For each component it produces a data frame with columns:

• x : sample IDs for the x axis, their factor order is the same as on the columns of input matrix
• y : expression values from the matrix
• . . . : sample annotation columns from the annotation table that can be displayed on figure as colors.

Examples

## Not run: 
# data(gs_limma)
# data(tissue_example)
# 
# # Add just expression without annotations
# gs_limma_exp1 = add_expression.gosummaries(gs_limma, exp = 
# tissue_example$exp)
# 
# print(gs_limma_exp1)
# 
# # Add expression with annotations
# gs_limma_exp2 = add_expression.gosummaries(gs_limma, exp = 
# tissue_example$exp, annotation = tissue_example$annot)
# 
# print(gs_limma_exp1)
# ## End(Not run)