3.3 scRNA seq
is a module that can simulate reads consisting of only UMIs per each, or UMI+Genomic sequence per each. The general-purpose design gives the module this name. To achieve this purpose, a case-study CLI should look like below:
Gene-by-cell matrix¶
import tresor as ts
gbycell, _, _ = ts.spsimseq_sc(
R_root='D:/Programming/R/R-4.3.2/',
num_genes=10,
num_cells=10,
simulator='spsimseq',
sv_fpn=to('data/spsimseq_sc.h5'),
)
print(gbycell)
tresor gmat_sc \
-rfpn D:/Programming/R/R-4.3.2/ \
-ncell 10 \
-ngene 10 \
-gsimulator spsimseq \
-wd ./tresor/data/spsimseq_sc.h5 \
-is True \
-vb True
Output¶
12/12/2023 00:37:15 logger: =========>spsimseq is being used
SPsimSeq package version 1.12.0
R[write to console]: Estimating featurewise correlations ...
R[write to console]: Selecting candidate DE genes ...
R[write to console]: Fitting zero probability model ...
R[write to console]: Estimating densities ...
R[write to console]: Configuring design ...
R[write to console]: Simulating data ...
R[write to console]: ...1 of 1
12/12/2023 00:37:23 logger: =========>spsimseq completes simulation
12/12/2023 00:37:23 logger: =========>spsimseq simu result:
$a
Sample_1 Sample_2 Sample_3 Sample_4 Sample_5 Sample_6 Sample_7 Sample_8
Gene_1 6 66 15 16 28 12 253 57
Gene_2 0 96 0 0 0 0 122 38
Gene_3 0 0 0 40 0 0 0 0
Gene_4 52 34 20 15 18 14 14 43
Gene_5 0 98 37 0 0 0 17 0
Gene_6 0 0 0 0 0 0 0 0
Gene_7 0 0 0 0 0 0 0 0
Gene_8 0 0 0 0 0 0 0 0
Gene_9 0 188 7 153 23 0 201 20
Gene_10 1 0 0 0 0 0 31 0
Sample_9 Sample_10
Gene_1 5 6
Gene_2 4 6
Gene_3 0 7
Gene_4 1 1
Gene_5 0 0
Gene_6 0 0
Gene_7 0 0
Gene_8 0 0
Gene_9 0 60
Gene_10 0 3
$b
Batch Group sim.Lib.Size
Sample_1 1 1 543
Sample_2 1 1 1980
Sample_3 1 1 950
Sample_4 1 1 1098
Sample_5 1 1 711
Sample_6 1 2 147
Sample_7 1 2 1568
Sample_8 1 2 1425
Sample_9 1 2 933
Sample_10 1 2 475
$c
DE.ind source.ID
Gene_1 TRUE ENSG00000138160
Gene_2 TRUE ENSG00000138160
Gene_3 FALSE ENSG00000066322
Gene_4 FALSE ENSG00000101608
Gene_5 FALSE ENSG00000130066
Gene_6 FALSE ENSG00000196358
Gene_7 FALSE ENSG00000273674
Gene_8 FALSE ENSG00000269694
Gene_9 FALSE ENSG00000162992
Gene_10 FALSE ENSG00000142634
Gene_1 Gene_2 Gene_3 Gene_4 ... Gene_7 Gene_8 Gene_9 Gene_10
Cell_0 6.0 0.0 0.0 52.0 ... 0.0 0.0 0.0 1.0
Cell_1 66.0 96.0 0.0 34.0 ... 0.0 0.0 188.0 0.0
Cell_2 15.0 0.0 0.0 20.0 ... 0.0 0.0 7.0 0.0
Cell_3 16.0 0.0 40.0 15.0 ... 0.0 0.0 153.0 0.0
Cell_4 28.0 0.0 0.0 18.0 ... 0.0 0.0 23.0 0.0
Cell_5 12.0 0.0 0.0 14.0 ... 0.0 0.0 0.0 0.0
Cell_6 253.0 122.0 0.0 14.0 ... 0.0 0.0 201.0 31.0
Cell_7 57.0 38.0 0.0 43.0 ... 0.0 0.0 20.0 0.0
Cell_8 5.0 4.0 0.0 1.0 ... 0.0 0.0 0.0 0.0
Cell_9 6.0 6.0 7.0 1.0 ... 0.0 0.0 60.0 3.0
[10 rows x 10 columns]