... | ... |
@@ -30,7 +30,7 @@ LinkingTo: Rcpp, RcppEigen |
30 | 30 |
License: MIT + file LICENSE |
31 | 31 |
Encoding: UTF-8 |
32 | 32 |
LazyData: true |
33 |
-RoxygenNote: 7.1.1 |
|
33 |
+RoxygenNote: 7.1.2 |
|
34 | 34 |
BugReports: https://github.com/campbio/celda/issues |
35 | 35 |
biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian |
36 | 36 |
NeedsCompilation: yes |
... | ... |
@@ -495,22 +495,21 @@ setMethod( |
495 | 495 |
z = as.integer(res$z), |
496 | 496 |
pseudocount = 1e-20 |
497 | 497 |
) |
498 |
- |
|
498 |
+ |
|
499 | 499 |
# Speed up sparse matrix value assignment by cbind -> order recovery |
500 |
- |
|
501 |
- allCol <- paste0("col_", 1:ncol(estRmat)) |
|
500 |
+ allCol <- paste0("col_", seq_len(ncol(estRmat))) |
|
502 | 501 |
colnames(estRmat) <- allCol |
503 |
- |
|
502 |
+ |
|
504 | 503 |
subCol <- paste0("col_", which(batch == bat)) |
505 | 504 |
colnames(estRmat.temp) <- subCol |
506 |
- |
|
505 |
+ |
|
507 | 506 |
estRmat <- estRmat[, !(allCol %in% subCol)] |
508 | 507 |
estRmat <- cbind(estRmat, estRmat.temp) |
509 |
- |
|
508 |
+ |
|
510 | 509 |
# Recover order |
511 | 510 |
estRmat <- estRmat[, allCol] |
512 |
- |
|
513 |
- #(Old method) estRmat[seq(nrow(counts)), which(batch == bat)] <- estRmat.temp |
|
511 |
+ |
|
512 |
+ ##estRmat[seq(nrow(counts)), which(batch == bat)] <- estRmat.temp |
|
514 | 513 |
dimnames(estRmat) <- list(geneNames, allCellNames) |
515 | 514 |
|
516 | 515 |
resBatch[[bat]] <- list( |