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Update modeling.R #203
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Update modeling.R #203
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sqjin
approved these changes
May 20, 2021
sqjin
reviewed
May 20, 2021
| @@ -49,7 +49,7 @@ netAnalysis_contribution <- function(object, signaling, signaling.name = NULL, w | |||
| pairLR <- pairLR[pairLR.name.use,] | |||
| } | |||
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| prob <- prob[,,pairLR.name.use] | |||
| prob <- prob[,,pairLR.name.use, drop=FALSE] | |||
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This is not necessary as we have if (length(dim(prob)) == 2) below.
sqjin
reviewed
May 20, 2021
R/modeling.R
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| @@ -375,7 +375,7 @@ computeCommunProbPathway <- function(object = NULL, net = NULL, pairLR.use = NUL | |||
| group <- factor(pairLR.use$pathway_name, levels = pathways) | |||
| prob.pathways <- aperm(apply(prob, c(1, 2), by, group, sum), c(2, 3, 1)) | |||
| pathways.sig <- pathways[apply(prob.pathways, 3, sum) != 0] | |||
| prob.pathways.sig <- prob.pathways[,,pathways.sig] | |||
| prob.pathways.sig <- prob.pathways[,,pathways.sig, drop=FALSE] | |||
| idx <- sort(apply(prob.pathways.sig, 3, sum), decreasing=TRUE, index.return = TRUE)$ix | |||
| pathways.sig <- pathways.sig[idx] | |||
| prob.pathways.sig <- prob.pathways.sig[, , idx] | |||
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Can you also change line 381 prob.pathways.sig <- prob.pathways.sig[, , idx] to prob.pathways.sig <- prob.pathways.sig[, , idx, drop=FALSE]
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@stemangiola Thanks for your contribution. I made two comments. Can you please edit them and then I will merge these pull requests. |
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In my dataset, the third dimension is 1, so drop=F avoids software crash.
Could you also please advise whether this is sometimes expected?