Hey @Rachael-rq ,
One of the examples for this function is not quite right; I know it is just an example, but we should not swap the up and down sets of the TGFb-EMT signature to generate a new score data frame; it may confuse people. Here is what you have written:
# For illustration of the function, we generate scoredf1 using
# upSet = tgfb_gs_dn, downSet = tgfb_gs_up,
# generate scoredf2 using upSet = tgfb_gs_dn, downSet = tgfb_gs_up
scoredf1 <- simpleScore(rankData, upSet = tgfb_gs_up, downSet = tgfb_gs_dn)
scoredf2 <- simpleScore(rankData, upSet = tgfb_gs_dn, downSet = tgfb_gs_up)
plotScoreLandscape(scoredf1, scoredf2, scorenames = c('tgfb_gs',
'tgfb_gs_reverse'))
How about if we remove the above example and only go with the CCLE and TCGA examples that you have also already included? Which is like:
So that we only need to mention that for the epithelial and mesenchymal signatures without the down set, we need to set downSet = NULL in the simpleScore function.
What do you thinks @bhuvad ?
Cheers,
Sepideh
Hey @Rachael-rq , One of the examples for this function is not quite right; I know it is just an example, but we should not swap the up and down sets of the TGFb-EMT signature to generate a new score data frame; it may confuse people. Here is what you have written:
How about if we remove the above example and only go with the CCLE and TCGA examples that you have also already included? Which is like:
So that we only need to mention that for the epithelial and mesenchymal signatures without the down set, we need to set
downSet = NULL
in the simpleScore function. What do you thinks @bhuvad ? Cheers, Sepideh