pathway_vectorization: Vectorization of pathways

In github-gs/QPA: Quantitative Pathway Analysis

Description

This function vectorizes pathways by creating pathway-gene profile.

Usage

pathway_vectorization(expression_profile,condition,group1,group2,pathway_info)

Arguments

expression_profile	Gene expression profile contains gene expression. Rownames are entrez IDs. Colnames are sample names.
condition	A vector contains group information of samples. For example, condition<-c(type1,type1,type2,type2) of four samples.
group1	Group1 to be compared.
group2	Group1 to be compared.
pathway_info	A list containing pathway information to be compared, which can be generated by the merge_pathway function.

Value

Return a dataframe which contains pathway-gene information. Colnames are pathways' names, rownames are genes' names and the value of each element is Foldchange between two groups.

Examples

data(example)
group1='Treatment'
group2='Model'
group3='Control'
Treatment_profile=pathway_vectorize(expression_profile,condition,group1,group2,pathway_info)
Model_profile=pathway_vectorize(expression_profile,condition,group2,group3,pathway_info)

github-gs/QPA documentation built on Sept. 11, 2019, 9:46 a.m.