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Table 1 Time in seconds for distance matrix calculation, L2 distance, serial execution

From: Scellpam: an R package/C++ library to perform parallel partitioning around medoids on scRNAseq data sets

 

R package

Sample

amap

parallelDist

cluster

stats

scellpam

scellpam

size

(Dist)

(pdist)

(dist)

(daisy)

(double, full)

(float, sparse)

8879

20980

4469

10338

10477

4049

2079

17758

155651

68326

59804

59467

16073

8200

35516

196906

273738

541886

516625

64382

32956

71032

(\(*1\))

551527

(\(*2\))

2214564

256678

131474

  1. (\(*1\)) Error in Dist(data, method = ”euclidean”, nbproc = 128, diag = FALSE: Long vectors (argument 4) are not supported in.C
  2. (\(*2\)) Error in daisy(data, metric = dtype, stand = FALSE): long vectors (argument 11) are not supported in.Fortran Execution halted
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BMC Bioinformatics

ISSN: 1471-2105

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