drawAHeatMap: Draw a heatmap for the genes of a pathway

In LncPath: Identifying the Pathways Regulated by LncRNA Sets of Interest

Description

Draw a heatmap for the genes of a certain pathway based on the expression profile user specified.

Usage

drawAHeatMap(Result, Name, PCExpr, Labels)

Arguments

Result	A lncPath object come from the lncPath function.
Name	A string, the name of the pathway to be plot.
PCExpr	A data frame, the expression profile to be plotted.
Labels	A vector of 0 and 1, 0 indicates control and 1 indicates case.

Details

Draw a heatmap of the genes of a pathway based on the expression profile. The rows of heatmap are genes ranked by their weights and the columns of heatmap are samples ordered the same as the expression profile.

Author(s)

Junwei Han <[e-mail]>, Zeguo Sun <[e-mail]>

References

Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. et al. (2005) Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A, 102, 15545-15550.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

Result <- getExampleData("Result")
Profile <- getExampleData("Profile")
Labels <- getExampleData("Labels")
drawAHeatMap(Result, "KEGG_RIBOSOME", Profile, Labels)

LncPath documentation built on May 2, 2019, 11:03 a.m.