findDAR is giving NA error

[galib36]

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)

[galib36]

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.

[r3fang]

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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[JihedC]

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.

Could you explain please? I get the same issue and can't figure out how to solve it