TopPathwayKeggToLatex:

In cherkaos/MetabToPathways: Query metabolites to find their pathways, for multiple databases (Kegg, SMPDB, HMDB and Biocyc)

Usage

TopPathwayKeggToLatex(puchem, name, top = 20, index = 1)

Arguments

puchem
name
top
index

Author(s)

Sarah Cherkaoui

Examples

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

## The function is currently defined as
function (puchem, name, top = 20, index = 1) 
{
    Pathways <- TopPathKegg(puchem, name)
    Pathways <- Pathways[1:top, ]
    output <- capture.output(stargazer(as.data.frame(Pathways), 
        title = "Pathway Analysis", font.size = "scriptsize", 
        type = "latex", summary = FALSE, label = paste0("table:tab", 
            index + 1, seq = ""), table.placement = "h"))
    cat(paste(output, collapse = "\n"), "\n", file = "pathways.tex", 
        append = TRUE)
  }

cherkaos/MetabToPathways documentation built on May 13, 2019, 3:54 p.m.