vignettes/tut5_giotto_markers.Rmd
tut5_giotto_markers.Rmd
This tutorial starts from a pre-computed mini Giotto object, which
has already undergone pre-processing, dimensions reduction and
clustering steps. Currently provides 3 different methods to identify
marker genes:
- using a new Gini-index method
- using Scran
- using Mast
Each method can either identify marker genes between 2 selected (groups of) clusters or for each individual cluster.
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# between 2 groups
gini_markers = findGiniMarkers(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus',
group_1 = 1,
group_2 = 2)
# for each cluster
gini_markers = findGiniMarkers_one_vs_all(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus')
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Requires Scran to be installed.
# between 2 groups
scran_markers = findScranMarkers(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus',
group_1 = 1,
group_2 = 2)
# for each cluster
scran_markers = findScranMarkers_one_vs_all(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus')
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Requires Mast to be installed.
# between 2 groups
mast_markers = findMastMarkers(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus',
group_1 = 1,
group_2 = 2)
# for each cluster
mast_markers = findMastMarkers_one_vs_all(gobject = mini_giotto_single_cell,
cluster_column = 'leiden_clus')
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