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@ -18,7 +18,9 @@ First load the library and dependencies.
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library(Matrix)
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library(Seurat)
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library(qlcMatrix)
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library(FastCAR)
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library(pheatmap)
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library(ggplot2)
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library(gridExtra)
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```
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Specify the locations of the expression matrices
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@ -47,6 +49,31 @@ plot.ambient.profile(ambProfile)
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The actual effect on the chances of genes affecting your DE analyses can be determined and visualized with the following function
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```
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correctionEffectProfile = describe.correction.effect(allExpression, cellExpression, 50, 500, 10, 0.05)
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plot.correction.effect.chance(correctionEffectProfile)
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```
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How many reads will be removed of these genes can be visualized from the same profile
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```
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plot.correction.effect.removal(correctionEffectProfile)
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```
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Set the empty droplet cutoff and the contamination chance cutoff
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The empty droplet cutoff is the number of UMIs a droplet can contain at the most to be considered empty.
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@ -69,8 +96,8 @@ emptyDropletCutoff = recommend.empty.cutoff(ambProfile)
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```
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emptyDropletCutoff = 100
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contaminationChanceCutoff = 0.05
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emptyDropletCutoff = 150
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contaminationChanceCutoff = 0.005
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```
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Determine the ambient RNA profile and remove the ambient RNA from each cell
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@ -103,3 +130,11 @@ First fully working version of the R package
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Fixed function to write the corrected matrix to file.
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Added readout of which genes will be corrected for and how many reads will be removed per cell
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Added some input checks to functions
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### v0.2
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Fixed a bug that caused FastCAR to be incompatible with biobase libraries
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Added better profiling to determine the effect of different settings on the corrections
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Swapped base R plots for ggplot2 plots
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