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Fix bugs in importMultipleSources.R. Update QC documentation

rz2333 authored on 19/10/2020 02:08:45
Showing 2 changed files

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@@ -85,12 +85,12 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
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       }
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       for(assay in SummarizedExperiment::assayNames(newSce)) {
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-        if(!base::inherits(SummarizedExperiment::assay(sce, assay), "dgCMatrix") && !isTRUE(delayedArray)) {
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-          SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))
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+        if(!base::inherits(SummarizedExperiment::assay(newSce, assay), "dgCMatrix") && !isTRUE(delayedArray)) {
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+          SummarizedExperiment::assay(newSce, assay) <- .convertToMatrix(SummarizedExperiment::assay(newSce, assay))
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         }
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-        if(!base::inherits(SummarizedExperiment::assay(sce, assay), "DelayedArray") && isTRUE(delayedArray)) {
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-          SummarizedExperiment::assay(sce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(sce, assay))
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+        if(!base::inherits(SummarizedExperiment::assay(newSce, assay), "DelayedArray") && isTRUE(delayedArray)) {
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+          SummarizedExperiment::assay(newSce, assay) <- DelayedArray::DelayedArray(SummarizedExperiment::assay(newSce, assay))
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         }
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       }
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@@ -313,7 +313,7 @@ The usage of each argument is the same as running command line analysis. Here is
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 ```
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 docker run --rm -v /path/to/data:/SCTK_docker \
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--it campbio/sctk_qc:1.7.5 \
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+-it campbio/sctk_qc:1.7.6 \
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 -b /SCTK_docker/cellranger \
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 -P CellRangerV3 \
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 -s pbmc_100x100 \
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@@ -328,7 +328,7 @@ docker run --rm -v /path/to/data:/SCTK_docker \
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 The Singulatiry image can easily be built using Docker Hub as a source:
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 ```
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-singularity pull docker://campbio/sctk_qc:1.7.5
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+singularity pull docker://campbio/sctk_qc:1.7.6
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 ```
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 The usage of singleCellTK Singularity image is very similar to that of Docker. In Singularity 3.0+, the mount volume is [automatically overlaid](https://singularity.lbl.gov/docs-mount). 
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@@ -337,7 +337,7 @@ It's recommended to re-set the home directory when you run singularity. Singular
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 ```
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 singularity run --home=/PathToSanitizedHome \
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+--bind /PathToData:/data sctk_qc_1.7.6.sif \
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 -P CellRangerV3 \
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 -s gencodev34_pbmc_1k_v3 \
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 -b /data/gencodev34_pbmc_1k_v3
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@@ -358,7 +358,7 @@ Also, you might want to specify cpu architecture when run the Singularity image
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 #$ -pe omp 16
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 #$ -l cpu_arch=broadwell|haswell|skylake|cascadelake
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 singularity run --home=/PathToSanitizedHome \
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+--bind /PathToData:/data sctk_qc_1.7.6.sif \
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 -P CellRangerV3 \
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 -s gencodev34_pbmc_1k_v3 \
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 -b /data/gencodev34_pbmc_1k_v3