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| author | Hui Lan <lanhui@zjnu.edu.cn> | 2022-11-20 20:53:44 +0800 |
|---|---|---|
| committer | Hui Lan <lanhui@zjnu.edu.cn> | 2022-11-20 20:53:44 +0800 |
| commit | d42ed749e13ce6e9c6a1dd67bc7c6569b34ce35b (patch) | |
| tree | a143c35d0255e38003619e10fbb104002566a19c | |
| parent | fc7c809c2d0bc3de120c3836d2800b271f9be607 (diff) | |
Fix the following errors while running create_edges0B.py
~/brain/Code$ python3 update_rnaseq_info_json.py
Error in library(Rtsne) : there is no package called ‘Rtsne’
~/brain/Code$ Rscript correlation_per_tissue.R
Error in quantile.default(sd.1) :
missing values and NaN's not allowed if 'na.rm' is FALSE
| -rw-r--r-- | Code/correlation_per_tissue.R | 2 | ||||
| -rw-r--r-- | Code/knn_classify.R | 1 |
2 files changed, 2 insertions, 1 deletions
diff --git a/Code/correlation_per_tissue.R b/Code/correlation_per_tissue.R index d9aadf9..0a16d4f 100644 --- a/Code/correlation_per_tissue.R +++ b/Code/correlation_per_tissue.R @@ -77,7 +77,7 @@ for (ul in unique.label) { X <- as.matrix(X0[, index.rnaseq]) sd.1 <- apply(X, 1, sd) # sd of each row s0 <- apply(X, 1, function(c) sum(c==0)) # number of zeros in each row - sd.tau <- (quantile(sd.1)[1] + quantile(sd.1)[2]) / 2.0 # min SD + sd.tau <- (quantile(sd.1, na.rm=TRUE)[1] + quantile(sd.1, na.rm=TRUE)[2]) / 2.0 # min SD good <- sd.1 > max(sd.tau, 0.05) tf_good <- which( good & (all_genes %in% tfs) == T ) target_good <- which( good & (all_genes %in% targets) == T ) diff --git a/Code/knn_classify.R b/Code/knn_classify.R index 46df992..995ae7b 100644 --- a/Code/knn_classify.R +++ b/Code/knn_classify.R @@ -39,6 +39,7 @@ rowsum.tau <- dim(X)[2] # the gene's TPM value is at least 1 on average sd.val <- apply(X, 1, sd) sd.tau <- summary(sd.val)[3] # genes whose gene expression varies least are to be filtered index <- rowSums(X) > rowsum.tau & sd.val > 10 +index[is.na(index)] <- FALSE n.train <- dim(X)[2] X.3 <- log(cbind(X[index,], X.2[index,]) + 1) |