path_vec: Vectorization of pathways

In github-gs/Quantitative-pathway-analysis: Quantitative Pathway Analysis

Description

This function vectorizes pathway by creating pathway-gene profiles.

Usage

path_vec(nmerge_tab,condition,group1,group2,kg.sets)

Arguments

nmerge_tab	Gene expression profile. Rownames of the table are entrez IDs of genes. Colnames are sample names. The elements of the table are the expression of genes.
condition	The parameter is a vector which contains the condition information of the samples, such as condition<-c(type1,type1,type2,type2) of four samples.
group1	The condition of samples that be compared.
group2	The condition of samples that be compared.
kg.sets	A collection of gene sets. An exsample data showed in data/.

Value

The functions provide the following results:

path_vec

return a list which contain two dataframes. The dataframes are pathway-gene profile which are the quantitative result of pathways. Colnames of the table are pathways' name, rownames are the genes' name.

Examples

data(data)
## Not run: 
path_vec(table,condition,group1,group2,kg.sets)

## End(Not run)

github-gs/Quantitative-pathway-analysis documentation built on May 13, 2019, 12:18 p.m.