LncPath (version 1.1)

printSignifResult: Output the details of significant pathways

Description

Export all of the significant pathways into a specified location.

Usage

printSignifResult(Result, Threshold = 0.01, Path = ".", HeatPlot = FALSE, 
	PCExpr = "", Labels = "", Top = 0)

Arguments

Result

A lncPath object come from the lncPath function.

Threshold

Numeric, the FDR threshold for selecting signifcant pathways.

Path

String, the output directory.

HeatPlot

Logical, should the heatmaps be plotted.

PCExpr

A data frame, represents the expression profile of genes, the rownames must be gene names, must be set if HeatPlot is TRUE.

Labels

A vector of 0 and 1, 0 indicates control and 1 indicates case.

Top

An integer, indicates the number of the most significant pathways to be print, the Threshold will be ignored.

Details

For a result from the lncPath function, pritSignifResult will output all the details of significant pathways. Significant pathways can be defined by the threshold user submit or by ranks. The detail of pathways contains the running score plot , the gene sets detail and the heatmap of each pathway. For heatmap plot , the corresponding expression profile is needed. Considering a lot of files will be output, the output directory can be specified.

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

# NOT RUN {
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.
# }
# NOT RUN {
Result <- getExampleData("Result")
Profile <- getExampleData("Profile")
Labels <- getExampleData("Labels")
dir.create("Signif")
SignifReport(Result, Threshold = 0.01, Path = "Signif", HeatPlot = TRUE, Profile, Labels, Top = 30)
# }