collapsePathways

[tallulandrews]

There is a typo or something in the collapsePathways function as it uses a variable called "pathway" that is not defined anywhere in the function. This seems to have appeared sometime between the current version and version 1.8.1 as my computer with the older version runs just fine.

Best, Tallulah

[tallulandrews]

`collapsePathways <- function(fgseaRes, pathways, stats, pval.threshold=0.05, nperm=10/pval.threshold, gseaParam=1) { universe <- names(stats)

pathways <- pathways[fgseaRes$pathway]
pathways <- lapply(pathways, intersect, universe)

parentPathways <- setNames(rep(NA, length(pathways)), names(pathways))

for (i in seq_along(pathways)) {
    p <- names(pathways)[i]
    if (!is.na(parentPathways[p])) {
        next
    }

    pathwaysToCheck <- setdiff(names(which(is.na(parentPathways))), p)
    pathwaysUp <- fgseaRes[pathway %fin% pathwaysToCheck & ES >= 0][, pathway] #### This line and
    pathwaysDown <- fgseaRes[pathway %fin% pathwaysToCheck & ES < 0][, pathway] #### This line use "pathway" that is not defined

    if (length(pathwaysToCheck) == 0) {
        break
    }

    minPval <- setNames(rep(1, length(pathwaysToCheck)), pathwaysToCheck)

    u1 <- setdiff(universe, pathways[[p]])

    fgseaResUp1 <- fgseaSimple(pathways = pathways[pathwaysUp], stats=stats[u1],
                               nperm=nperm, maxSize=length(u1)-1, nproc=1,
                               gseaParam=gseaParam, scoreType = "pos")
    fgseaResDown1 <- fgseaSimple(pathways = pathways[pathwaysDown], stats=stats[u1],
                                 nperm=nperm, maxSize=length(u1)-1, nproc=1,
                                 gseaParam=gseaParam, scoreType = "neg")
    fgseaRes1 <- rbindlist(list(fgseaResUp1, fgseaResDown1), use.names = TRUE)

    minPval[fgseaRes1$pathway] <- pmin(minPval[fgseaRes1$pathway], fgseaRes1$pval)

    u2 <- pathways[[p]]

    fgseaResUp2 <- fgseaSimple(pathways = pathways[pathwaysUp], stats=stats[u2],
                               nperm=nperm, maxSize=length(u2)-1, nproc=1,
                               gseaParam=gseaParam, scoreType = "pos")
    fgseaResDown2 <- fgseaSimple(pathways = pathways[pathwaysDown], stats=stats[u2],
                                 nperm=nperm, maxSize=length(u2)-1, nproc=1,
                                 gseaParam=gseaParam, scoreType = "neg")
    fgseaRes2 <- rbindlist(list(fgseaResUp2, fgseaResDown2), use.names = TRUE)

    minPval[fgseaRes2$pathway] <- pmin(minPval[fgseaRes2$pathway], fgseaRes2$pval)

    parentPathways[names(which(minPval > pval.threshold))] <- p
}

return(list(mainPathways=names(which(is.na(parentPathways))),
            parentPathways=parentPathways))

} `

[assaron]

No, this is not a typo, it takes pathway column from fgseaRes, which is a data.table object.

Please, post an actual error that you get, with a reproducible example, if possible.