adjusting calls to funcs of backbone, adapting to recent code changes…
Federico Marini authored on 21/03/2022 23:06:28
• GitHub committed on 21/03/2022 23:06:28
| ... | ... |
@@ -399,16 +399,16 @@ ggs_backbone <- function(res_enrich, |
| 399 | 399 |
} |
| 400 | 400 |
|
| 401 | 401 |
if (bb_method == "sdsm") {
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| 402 |
- bbobj <- backbone::sdsm(bpm_for_backbone) |
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+ bbobj <- backbone::sdsm(bpm_for_backbone, alpha = NULL) |
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| 403 | 403 |
} else if (bb_method == "fdsm") {
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- bbobj <- backbone::fdsm(bpm_for_backbone, trials = 1000) |
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+ bbobj <- backbone::fdsm(bpm_for_backbone, trials = 1000, alpha = NULL) |
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| 405 | 405 |
} else if (bb_method == "fixedrow") {
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- bbobj <- backbone::fixedrow(bpm_for_backbone) |
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+ bbobj <- backbone::fixedrow(bpm_for_backbone, alpha = NULL) |
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| 407 | 407 |
} |
| 408 | 408 |
|
| 409 | 409 |
bbextracted <- backbone::backbone.extract(bbobj, |
| 410 | 410 |
alpha = bb_extract_alpha, |
| 411 |
- fwer = bb_extract_fwer |
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+ mtc = bb_extract_fwer |
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| 412 | 412 |
) |
| 413 | 413 |
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| 414 | 414 |
bbgraph <- igraph::graph_from_adjacency_matrix(bbextracted, mode = "undirected") |