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findDAR is giving NA error
When I am running findDAR
it gives me Error: NA counts not allowed. The command I used are
DARs = findDAR( obj=x.sp.filt, input.mat="pmat", cluster.pos=5, #cluster.neg=2, cluster.neg.method="knn", test.method="exactTest", bcv=0.4, #0.4 for human, 0.1 for mouse seed.use=10 )
and the traceback of the error shows
stop("NA counts not allowed", call. = FALSE)
.isAllZero(y)
mglmOneGroup(y1 + matrix(prior.count[j1], ntags, n1, byrow = TRUE), offset = offset.aug[j1], dispersion = dispersion)
exactTest(y, dispersion = bcv^2)
findDAR.default(obj = x.sp.filt, input.mat = "pmat", cluster.pos = 5, cluster.neg = 2, test.method = "exactTest", bcv = 0.4, seed.use = 10)
findDAR(obj = x.sp.filt, input.mat = "pmat", cluster.pos = 5, cluster.neg = 2, test.method = "exactTest", bcv = 0.4, seed.use = 10)
Sorry I found the solution, I was using createPmat
to add peaks-to-cells. But if I use the snaptools
command to do it then the error does not show up.
sounds great! Thank you for letting me know
-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego
On Sep 19, 2019, at 7:14 AM, galib36 [email protected] wrote:
Sorry I found the solution, I was using createPmat to add peaks-to-cells. But if I use the snaptools command to do it then the error does not show up.
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Sorry I found the solution, I was using
createPmat
to add peaks-to-cells. But if I use thesnaptools
command to do it then the error does not show up.
Could you explain please? I get the same issue and can't figure out how to solve it