r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
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error In runKNN() #240

Open 1221li opened 2 years ago

1221li commented 2 years ago

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