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error In runKNN() #240

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1221li opened this issue Dec 9, 2021 · 0 comments
Open

error In runKNN() #240

1221li opened this issue Dec 9, 2021 · 0 comments

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@1221li
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1221li commented Dec 9, 2021

Dear author and friends, I have a problem to consult. This problem has been bothering me for two days, but I still have no solution。
When I run runKNN (), it keeps showing the following error, but I have no "NA" in my data, I am looking forward to your answers!

x.sp_knn = runKNN(obj=x.sp_test,eigs.dims=1:20,k=15)
Epoch: checking input parameters
Epoch: computing nearest neighbor graph
Error in nn2(data = data.use, k = k, searchtype = "standard", eps = nn.eps) :
NA/NaN/Inf in foreign function call (arg 1)
head(x.sp_test@metaData)
y total duplicate chimeric unmapped lowmapq mitochondrial
34 AAACGAAAGACCTATC 2330 1092 25 28 313 2
43 AAACGAAAGAGAACCC 1707 737 18 82 382 15
323 AAACGAACAATGCCAT 1749 706 115 93 521 13
421 AAACGAACAGCGCGTT 247579 108241 2016 3160 32193 4
681 AAACGAAGTGTTGTTG 881 310 23 64 213 3
825 AAACGAATCCCACGGA 2278 768 113 76 731 14
passed_filters cell_id is__cell_barcode TSS_fragments
34 870 0 0 40
43 473 0 0 25
323 301 0 0 20
421 101965 0 1 22290
681 268 0 0 45
825 576 0 0 58
DNase_sensitive_region_fragments enhancer_region_fragments
34 0 0
43 0 0
323 0 0
421 0 0
681 0 0
825 0 0
promoter_region_fragments on_target_fragments blacklist_region_fragments
34 0 40 0
43 0 25 0
323 0 20 0
421 0 22290 0
681 0 45 0
825 0 58 0
peak_region_fragments peak_region_cutsites logUMI promoter_ratio sample
34 116 212 2.940018 0.001148105626 63
43 80 149 2.675778 0.002109704641 63
323 57 109 2.480007 0.003311258278 63
421 64239 122333 5.008455 0.000009807191 63
681 66 127 2.429752 0.003717472119 63
825 90 161 2.761176 0.001733102253 63
landmark
34 1
43 1
323 1
421 1
681 1
825 1

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