8000 CRITICAL MISTAKE IN createCARDObject FUNCTION CODE · Issue #84 · YMa-lab/CARD · GitHub
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CRITICAL MISTAKE IN createCARDObject FUNCTION CODE #84

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karJac opened this issue Feb 18, 2025 · 0 comments
Open

CRITICAL MISTAKE IN createCARDObject FUNCTION CODE #84

karJac opened this issue Feb 18, 2025 · 0 comments

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@karJac
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karJac commented Feb 18, 2025

Hi,

In the createCARDObject function there is a mistake in the logic in the lines:

spatial_countMat = spatial_countMat[rowSums(spatial_countMat >
0) > minCountSpot, ]
spatial_countMat = spatial_countMat[, (colSums(spatial_countMat) >=
minCountGene & colSums(spatial_countMat) <= 1e+06)]

Looking at the object which is input to these function, you apply the genes threshold for minimum number of read to the cells and the cells threshold to the genes.

spatial_countMat[1:5,1:5]
5 x 5 sparse Matrix of class "dgCMatrix"
s_008um_00433_00599-1 s_008um_00511_00539-1 s_008um_00474_00567-1
ISG15 . . .
ANKRD65 . . .
VWA1 . . .
MEGF6 . . .
TPRG1L . . .

Best,
Karol
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