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gs = GSEA(args.data, args.gmt, args.cls, args.outdir,
args.mins, args.maxs, args.n, args.weight,
args.type, args.method, args.ascending, args.threads,
args.figsize, args.format, args.graph, args.noplot, args.seed, args.verbose)
gs.run()
elif subcommand == "prerank":
from .gsea import Prerank
pre = Prerank(args.rnk, args.gmt, args.outdir, args.label[0], args.label[1],
args.mins, args.maxs, args.n, args.weight, args.ascending, args.threads,
args.figsize, args.format, args.graph, args.noplot, args.seed, args.verbose)
pre.run()
elif subcommand == "ssgsea":
from .gsea import SingleSampleGSEA
ss = SingleSampleGSEA(data=args.data, gene_sets=args.gmt, outdir=args.outdir,
sample_norm_method=args.norm,
min_size=args.mins, max_size=args.maxs, permutation_num=args.n,
weighted_score_type=args.weight, scale=args.scale,
ascending=args.ascending, processes=args.threads,
figsize=args.figsize, format=args.format, graph_num=args.graph,
no_plot=args.noplot, seed=args.seed, verbose=args.verbose)
ss.run()
elif subcommand == "enrichr":
# calling enrichr API
from .enrichr import Enrichr
enr = Enrichr(gene_list=args.gene_list, descriptions=args.descrip,
gene_sets=args.library, organism=args.organism,
outdir=args.outdir, format=args.format, cutoff=args.thresh,
background=args.bg, figsize=args.figsize,
top_term=args.term, no_plot=args.noplot, verbose=args.verbose)
and normalized enrichment score by obj.res2d.
if permutation_num > 0, additional results contain::
| {es: enrichment score,
| nes: normalized enrichment score,
| p: P-value,
| fdr: FDR,
| size: gene set size,
| matched_size: genes matched to the data,
| genes: gene names from the data set
| ledge_genes: leading edge genes, if permutation_num >0}
"""
ss = SingleSampleGSEA(data, gene_sets, outdir, sample_norm_method, min_size, max_size,
permutation_num, weighted_score_type, scale, ascending,
processes, figsize, format, graph_num, no_plot, seed, verbose)
ss.run()
return ss