P278949/FastCAR
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Fixed a bug where base rowSums were used instead of Matrix rowSums

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Marijn 2020-03-26 15:10:24 +01:00
parent c7a8c6a881
commit 92cb2a655b
2 changed files with 2 additions and 4 deletions
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4
R/FastCAR_Base.R
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@ -47,7 +47,7 @@ determine.background.to.remove = function(fullCellMatrix, cellMatrix, emptyDropl
# droplets that are empty but not unused barcodes, unused barcodes have zero reads assigned to them. # droplets that are empty but not unused barcodes, unused barcodes have zero reads assigned to them.
nEmpty = table((Matrix::colSums(fullCellMatrix) < emptyDropletCutoff) &(Matrix::colSums(fullCellMatrix) > 0))[2] nEmpty = table((Matrix::colSums(fullCellMatrix) < emptyDropletCutoff) &(Matrix::colSums(fullCellMatrix) > 0))[2]
# rowSum on a logical statement returns the number of TRUE occurences # rowSum on a logical statement returns the number of TRUE occurences
occurences = rowSums(fullCellMatrix[,Matrix::colSums(fullCellMatrix) < emptyDropletCutoff] !=0) occurences = Matrix::rowSums(fullCellMatrix[,Matrix::colSums(fullCellMatrix) < emptyDropletCutoff] !=0)
#probability of a background read of a gene ending up in a cell #probability of a background read of a gene ending up in a cell
probabiltyCellContaminationPerGene = occurences / nEmpty probabiltyCellContaminationPerGene = occurences / nEmpty
@ -100,7 +100,7 @@ describe.ambient.RNA.sequence = function(fullCellMatrix, start, stop, by, contam
for(emptyCutoff in seq(start, stop, by)){ for(emptyCutoff in seq(start, stop, by)){
nEmpty = table((Matrix::colSums(fullCellMatrix) < emptyCutoff) &(Matrix::colSums(fullCellMatrix) > 0))[2] nEmpty = table((Matrix::colSums(fullCellMatrix) < emptyCutoff) &(Matrix::colSums(fullCellMatrix) > 0))[2]
occurences = rowSums(fullCellMatrix[,Matrix::colSums(fullCellMatrix) < emptyCutoff] !=0) occurences = Matrix::rowSums(fullCellMatrix[,Matrix::colSums(fullCellMatrix) < emptyCutoff] !=0)
#probability of a background read of a gene ending up in a cell #probability of a background read of a gene ending up in a cell
probabiltyCellContaminationPerGene = occurences / nEmpty probabiltyCellContaminationPerGene = occurences / nEmpty

2
README.md
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@ -84,8 +84,6 @@ write.corrected.matrix(cellMatrix, correctedMatrixFolder, ambientProfile)
``` ```
## Authors ## Authors
* **Marijn Berg** - m.berg@umcg.nl * **Marijn Berg** - m.berg@umcg.nl