comparison fgsea.R @ 2:17eb1e0d711f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea commit 7f92023de5d3d922ad6cfd22f4de263b56127a1c

1:101b208a3e1a

} else {
  pathways <- load(sets_file)
  pathways <- get(pathways)
}

fgseaRes <- fgsea(pathways, ranks, minSize=min_size, maxSize=max_size, nperm=n_perm)
fgseaRes <- fgseaRes[order(pval), ]
# Convert leadingEdge column from list to character to output
fgseaRes$leadingEdge <- sapply(fgseaRes$leadingEdge, toString)

2:17eb1e0d711f

} else {
  pathways <- load(sets_file)
  pathways <- get(pathways)
}

# need to set seed for reproducibility https://github.com/ctlab/fgsea/issues/12
set.seed(42)
fgseaRes <- fgsea(pathways, ranks, minSize=min_size, maxSize=max_size, nperm=n_perm)
fgseaRes <- fgseaRes[order(pval), ]
# Convert leadingEdge column from list to character to output
fgseaRes$leadingEdge <- sapply(fgseaRes$leadingEdge, toString)