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Marijn 2020-03-26 12:05:04 +01:00
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README.md
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@ -54,7 +54,8 @@ fullMatrix = read.full.matrix(fullMatrixFolder)
``` ```
The following functions give an idea of the effect that different settings have on the ambient RNA profile The following functions give an idea of the effect that different settings have on the ambient RNA profile.
Plotting the number of empty droplets, the number of genes identified in the ambient RNA, and the number of genes that will be corrected for at different UMI cutoffs,
``` ```
ambProfile = describe.ambient.RNA.sequence(fullCellMatrix = fullMatrix, start = 10, stop = 500, by = 10, contaminationChanceCutoff = 0.05) ambProfile = describe.ambient.RNA.sequence(fullCellMatrix = fullMatrix, start = 10, stop = 500, by = 10, contaminationChanceCutoff = 0.05)
@ -65,7 +66,17 @@ plot.ambient.profile(ambProfile)
Set Set the empty droplet cutoff and the contamination chance cutoff
The empty droplet cutoff is the number of UMIs a droplet can contain at the most to be considered empty.
100 works fine but we tested this method in only one tissue. For other tissues this might not be the.
Increasing this number also increases the highest possible value of expression of a given gene.
As the correction will remove this value from every cell it is adviced not to set this too high and thereby overcorrect the expression in lowly expressing cells.
The contamination chance cutoff is the allowed probability of a gene contaminating a cell.
As we developed FastCAR specifically for differential expression analyses between groups we suggest setting this such that not enough cells could be contaminated to affect this.
In a cluster of a thousand cells divided into two groups there would be 2-3 cells per group with ambient RNA contamination of any given gene.
Such low cell numbers are disregarded for differential expression analyses.
``` ```