Calculate intra correlation between cluster or samples

Source: R/correlation_filtering_clustering.R

Calculate intra correlation between cluster or samples

intra_correlation_scExp(scExp_cf, by = c("sample_id", "cell_cluster")[1])

Arguments

scExp_cf

A SingleCellExperiment
by

On which feature to calculate correlation ("sample_id" or "cell_cluster")

Value

A data.frame of cell average intra-correlation

Examples

data(scExp)
intra_correlation_scExp(scExp, by = "sample_id")

#>                                          sample_id intra_corr
#> scChIP_Jurkat_K4me3_BC1062721  scChIP_Jurkat_K4me3 0.26674676
#> scChIP_Jurkat_K4me3_BC12143233 scChIP_Jurkat_K4me3 0.13754858
#> scChIP_Jurkat_K4me3_BC13415329 scChIP_Jurkat_K4me3 0.24448606
#> scChIP_Jurkat_K4me3_BC15476065 scChIP_Jurkat_K4me3 0.20750927
#> scChIP_Jurkat_K4me3_BC16748833 scChIP_Jurkat_K4me3 0.15621435
#> scChIP_Jurkat_K4me3_BC17648641 scChIP_Jurkat_K4me3 0.15854069
#> scChIP_Jurkat_K4me3_BC20721121 scChIP_Jurkat_K4me3 0.21318096
#> scChIP_Jurkat_K4me3_BC21672769 scChIP_Jurkat_K4me3 0.12183935
#> scChIP_Jurkat_K4me3_BC22586401 scChIP_Jurkat_K4me3 0.19479498
#> scChIP_Jurkat_K4me3_BC23141473 scChIP_Jurkat_K4me3 0.12385641
#> scChIP_Jurkat_K4me3_BC2340865  scChIP_Jurkat_K4me3 0.20327234
#> scChIP_Jurkat_K4me3_BC23851969 scChIP_Jurkat_K4me3 0.09764539
#> scChIP_Jurkat_K4me3_BC24108961 scChIP_Jurkat_K4me3 0.15148547
#> scChIP_Jurkat_K4me3_BC24665185 scChIP_Jurkat_K4me3 0.13827676
#> scChIP_Jurkat_K4me3_BC26968033 scChIP_Jurkat_K4me3 0.22201719
#> scChIP_Jurkat_K4me3_BC28166785 scChIP_Jurkat_K4me3 0.09713911
#> scChIP_Jurkat_K4me3_BC31515361 scChIP_Jurkat_K4me3 0.20987389
#> scChIP_Jurkat_K4me3_BC34973569 scChIP_Jurkat_K4me3 0.25552524
#> scChIP_Jurkat_K4me3_BC35823937 scChIP_Jurkat_K4me3 0.23568537
#> scChIP_Jurkat_K4me3_BC37576129 scChIP_Jurkat_K4me3 0.04476699
#> scChIP_Jurkat_K4me3_BC38512993 scChIP_Jurkat_K4me3 0.11549025
#> scChIP_Jurkat_K4me3_BC39310561 scChIP_Jurkat_K4me3 0.20951857
#> scChIP_Jurkat_K4me3_BC39912865 scChIP_Jurkat_K4me3 0.18960920
#> scChIP_Jurkat_K4me3_BC40220065 scChIP_Jurkat_K4me3 0.05847309
#> scChIP_Jurkat_K4me3_BC41338177 scChIP_Jurkat_K4me3 0.12188603
#> scChIP_Jurkat_K4me3_BC41719873 scChIP_Jurkat_K4me3 0.17395175
#> scChIP_Jurkat_K4me3_BC43343425 scChIP_Jurkat_K4me3 0.12393970
#> scChIP_Jurkat_K4me3_BC44502337 scChIP_Jurkat_K4me3 0.14698444
#> scChIP_Jurkat_K4me3_BC47439073 scChIP_Jurkat_K4me3 0.19445546
#> scChIP_Jurkat_K4me3_BC47520577 scChIP_Jurkat_K4me3 0.08044842
#> scChIP_Jurkat_K4me3_BC47570113 scChIP_Jurkat_K4me3 0.23719831
#> scChIP_Jurkat_K4me3_BC4894657  scChIP_Jurkat_K4me3 0.09454936
#> scChIP_Jurkat_K4me3_BC50167009 scChIP_Jurkat_K4me3 0.18672516
#> scChIP_Jurkat_K4me3_BC54146401 scChIP_Jurkat_K4me3 0.17115088
#> scChIP_Jurkat_K4me3_BC56298337 scChIP_Jurkat_K4me3 0.07789120
#> scChIP_Jurkat_K4me3_BC57367393 scChIP_Jurkat_K4me3 0.21973984
#> scChIP_Jurkat_K4me3_BC57949537 scChIP_Jurkat_K4me3 0.19400677
#> scChIP_Jurkat_K4me3_BC60120097 scChIP_Jurkat_K4me3 0.16183239
#> scChIP_Jurkat_K4me3_BC61740385 scChIP_Jurkat_K4me3 0.20658225
#> scChIP_Jurkat_K4me3_BC67162081 scChIP_Jurkat_K4me3 0.13743437
#> scChIP_Jurkat_K4me3_BC67415425 scChIP_Jurkat_K4me3 0.15059885
#> scChIP_Jurkat_K4me3_BC68083489 scChIP_Jurkat_K4me3 0.18844732
#> scChIP_Jurkat_K4me3_BC71253025 scChIP_Jurkat_K4me3 0.09437510
#> scChIP_Jurkat_K4me3_BC72501889 scChIP_Jurkat_K4me3 0.18869430
#> scChIP_Jurkat_K4me3_BC74529217 scChIP_Jurkat_K4me3 0.13890884
#> scChIP_Jurkat_K4me3_BC74612545 scChIP_Jurkat_K4me3 0.18544694
#> scChIP_Jurkat_K4me3_BC74736577 scChIP_Jurkat_K4me3 0.08868541
#> scChIP_Jurkat_K4me3_BC74865601 scChIP_Jurkat_K4me3 0.19621915
#> scChIP_Jurkat_K4me3_BC76074433 scChIP_Jurkat_K4me3 0.04622832
#> scChIP_Jurkat_K4me3_BC81515233 scChIP_Jurkat_K4me3 0.13213568
#> scChIP_Jurkat_K4me3_BC8618497  scChIP_Jurkat_K4me3 0.24223646
#> scChIP_Ramos_K4me3_BC14774209   scChIP_Ramos_K4me3 0.24586848
#> scChIP_Ramos_K4me3_BC17271937   scChIP_Ramos_K4me3 0.17041963
#> scChIP_Ramos_K4me3_BC19205185   scChIP_Ramos_K4me3 0.08941012
#> scChIP_Ramos_K4me3_BC20312449   scChIP_Ramos_K4me3 0.23472063
#> scChIP_Ramos_K4me3_BC20546113   scChIP_Ramos_K4me3 0.16127786
#> scChIP_Ramos_K4me3_BC21132481   scChIP_Ramos_K4me3 0.11098171
#> scChIP_Ramos_K4me3_BC22013857   scChIP_Ramos_K4me3 0.11337821
#> scChIP_Ramos_K4me3_BC23778049   scChIP_Ramos_K4me3 0.24296412
#> scChIP_Ramos_K4me3_BC25192897   scChIP_Ramos_K4me3 0.17649749
#> scChIP_Ramos_K4me3_BC26053537   scChIP_Ramos_K4me3 0.12123130
#> scChIP_Ramos_K4me3_BC28858273   scChIP_Ramos_K4me3 0.10712850
#> scChIP_Ramos_K4me3_BC28860865   scChIP_Ramos_K4me3 0.10499888
#> scChIP_Ramos_K4me3_BC29455681   scChIP_Ramos_K4me3 0.11269842
#> scChIP_Ramos_K4me3_BC35562721   scChIP_Ramos_K4me3 0.27319391
#> scChIP_Ramos_K4me3_BC35820481   scChIP_Ramos_K4me3 0.19828586
#> scChIP_Ramos_K4me3_BC36249793   scChIP_Ramos_K4me3 0.22225397
#> scChIP_Ramos_K4me3_BC3676513    scChIP_Ramos_K4me3 0.28419852
#> scChIP_Ramos_K4me3_BC37639681   scChIP_Ramos_K4me3 0.08445288
#> scChIP_Ramos_K4me3_BC38001121   scChIP_Ramos_K4me3 0.21793680
#> scChIP_Ramos_K4me3_BC39188833   scChIP_Ramos_K4me3 0.13779503
#> scChIP_Ramos_K4me3_BC40418401   scChIP_Ramos_K4me3 0.13307877
#> scChIP_Ramos_K4me3_BC40682209   scChIP_Ramos_K4me3 0.05292964
#> scChIP_Ramos_K4me3_BC40866433   scChIP_Ramos_K4me3 0.17448869
#> scChIP_Ramos_K4me3_BC42021505   scChIP_Ramos_K4me3 0.05849924
#> scChIP_Ramos_K4me3_BC42290113   scChIP_Ramos_K4me3 0.20643557
#> scChIP_Ramos_K4me3_BC46043233   scChIP_Ramos_K4me3 0.15601864
#> scChIP_Ramos_K4me3_BC4666369    scChIP_Ramos_K4me3 0.16476991
#> scChIP_Ramos_K4me3_BC47331841   scChIP_Ramos_K4me3 0.11492886
#> scChIP_Ramos_K4me3_BC50190721   scChIP_Ramos_K4me3 0.15200492
#> scChIP_Ramos_K4me3_BC50825473   scChIP_Ramos_K4me3 0.12276246
#> scChIP_Ramos_K4me3_BC5271265    scChIP_Ramos_K4me3 0.14888421
#> scChIP_Ramos_K4me3_BC56576929   scChIP_Ramos_K4me3 0.20697213
#> scChIP_Ramos_K4me3_BC57761665   scChIP_Ramos_K4me3 0.18442510
#> scChIP_Ramos_K4me3_BC58075105   scChIP_Ramos_K4me3 0.12727939
#> scChIP_Ramos_K4me3_BC58556353   scChIP_Ramos_K4me3 0.17215729
#> scChIP_Ramos_K4me3_BC58852705   scChIP_Ramos_K4me3 0.13703853
#> scChIP_Ramos_K4me3_BC59649601   scChIP_Ramos_K4me3 0.07410327
#> scChIP_Ramos_K4me3_BC60971713   scChIP_Ramos_K4me3 0.13640647
#> scChIP_Ramos_K4me3_BC66549409   scChIP_Ramos_K4me3 0.13264261
#> scChIP_Ramos_K4me3_BC66908353   scChIP_Ramos_K4me3 0.15944375
#> scChIP_Ramos_K4me3_BC6733729    scChIP_Ramos_K4me3 0.20461844
#> scChIP_Ramos_K4me3_BC68560129   scChIP_Ramos_K4me3 0.16570578
#> scChIP_Ramos_K4me3_BC68914753   scChIP_Ramos_K4me3 0.04884334
#> scChIP_Ramos_K4me3_BC71198401   scChIP_Ramos_K4me3 0.24627727
#> scChIP_Ramos_K4me3_BC7302049    scChIP_Ramos_K4me3 0.18809601
#> scChIP_Ramos_K4me3_BC73327681   scChIP_Ramos_K4me3 0.22252431
#> scChIP_Ramos_K4me3_BC74665729   scChIP_Ramos_K4me3 0.14637619
#> scChIP_Ramos_K4me3_BC74863489   scChIP_Ramos_K4me3 0.09126382
#> scChIP_Ramos_K4me3_BC75159073   scChIP_Ramos_K4me3 0.16292262
#> scChIP_Ramos_K4me3_BC76624129   scChIP_Ramos_K4me3 0.19183388
#> scChIP_Ramos_K4me3_BC77629153   scChIP_Ramos_K4me3 0.13447767
#> scChIP_Ramos_K4me3_BC77810689   scChIP_Ramos_K4me3 0.25636215
#> scChIP_Ramos_K4me3_BC78287521   scChIP_Ramos_K4me3 0.16706932
#> scChIP_Ramos_K4me3_BC78985057   scChIP_Ramos_K4me3 0.12944458
#> scChIP_Ramos_K4me3_BC9280513    scChIP_Ramos_K4me3 0.14379450
intra_correlation_scExp(scExp, by = "cell_cluster")

#>                                cell_cluster  intra_corr
#> scChIP_Jurkat_K4me3_BC1062721            C1  0.27471236
#> scChIP_Jurkat_K4me3_BC12143233           C1  0.13928429
#> scChIP_Jurkat_K4me3_BC13415329           C1  0.24794425
#> scChIP_Jurkat_K4me3_BC15476065           C1  0.21526889
#> scChIP_Jurkat_K4me3_BC16748833           C1  0.16259603
#> scChIP_Jurkat_K4me3_BC17648641           C1  0.16958444
#> scChIP_Jurkat_K4me3_BC20721121           C1  0.21992816
#> scChIP_Jurkat_K4me3_BC21672769           C1  0.13589452
#> scChIP_Jurkat_K4me3_BC22586401           C1  0.19704704
#> scChIP_Jurkat_K4me3_BC23141473           C1  0.12699263
#> scChIP_Jurkat_K4me3_BC2340865            C1  0.22056782
#> scChIP_Jurkat_K4me3_BC23851969           C1  0.09710053
#> scChIP_Jurkat_K4me3_BC24108961           C1  0.16057456
#> scChIP_Jurkat_K4me3_BC24665185           C1  0.15102076
#> scChIP_Jurkat_K4me3_BC26968033           C1  0.23324493
#> scChIP_Jurkat_K4me3_BC28166785           C1  0.11145156
#> scChIP_Jurkat_K4me3_BC31515361           C1  0.22196650
#> scChIP_Jurkat_K4me3_BC34973569           C1  0.27288936
#> scChIP_Jurkat_K4me3_BC35823937           C1  0.24114355
#> scChIP_Jurkat_K4me3_BC37576129           C1  0.05470322
#> scChIP_Jurkat_K4me3_BC38512993           C1  0.12671598
#> scChIP_Jurkat_K4me3_BC39310561           C1  0.21636698
#> scChIP_Jurkat_K4me3_BC39912865           C1  0.19325828
#> scChIP_Jurkat_K4me3_BC41719873           C1  0.19179453
#> scChIP_Jurkat_K4me3_BC43343425           C1  0.13382083
#> scChIP_Jurkat_K4me3_BC44502337           C1  0.15095142
#> scChIP_Jurkat_K4me3_BC47439073           C1  0.20142051
#> scChIP_Jurkat_K4me3_BC47570113           C1  0.24930595
#> scChIP_Jurkat_K4me3_BC4894657            C1  0.10586240
#> scChIP_Jurkat_K4me3_BC50167009           C1  0.19159519
#> scChIP_Jurkat_K4me3_BC54146401           C1  0.17119014
#> scChIP_Jurkat_K4me3_BC57367393           C1  0.22591278
#> scChIP_Jurkat_K4me3_BC57949537           C1  0.20052500
#> scChIP_Jurkat_K4me3_BC60120097           C1  0.16593912
#> scChIP_Jurkat_K4me3_BC61740385           C1  0.21921194
#> scChIP_Jurkat_K4me3_BC67162081           C1  0.14443616
#> scChIP_Jurkat_K4me3_BC67415425           C1  0.15872283
#> scChIP_Jurkat_K4me3_BC68083489           C1  0.18954541
#> scChIP_Jurkat_K4me3_BC71253025           C1  0.10165444
#> scChIP_Jurkat_K4me3_BC72501889           C1  0.20212281
#> scChIP_Jurkat_K4me3_BC74529217           C1  0.15059705
#> scChIP_Jurkat_K4me3_BC74612545           C1  0.19476862
#> scChIP_Jurkat_K4me3_BC74736577           C1  0.09188375
#> scChIP_Jurkat_K4me3_BC74865601           C1  0.21226421
#> scChIP_Jurkat_K4me3_BC76074433           C1  0.05564977
#> scChIP_Jurkat_K4me3_BC81515233           C1  0.13068877
#> scChIP_Jurkat_K4me3_BC8618497            C1  0.25744262
#> scChIP_Jurkat_K4me3_BC40220065           C2 -0.01305023
#> scChIP_Jurkat_K4me3_BC41338177           C2 -0.07957823
#> scChIP_Jurkat_K4me3_BC47520577           C2 -0.03061905
#> scChIP_Jurkat_K4me3_BC56298337           C2 -0.05735439
#> scChIP_Ramos_K4me3_BC14774209            C2  0.22784887
#> scChIP_Ramos_K4me3_BC17271937            C2  0.14939286
#> scChIP_Ramos_K4me3_BC19205185            C2  0.08562223
#> scChIP_Ramos_K4me3_BC20312449            C2  0.21056073
#> scChIP_Ramos_K4me3_BC20546113            C2  0.14866757
#> scChIP_Ramos_K4me3_BC21132481            C2  0.10517172
#> scChIP_Ramos_K4me3_BC22013857            C2  0.10543964
#> scChIP_Ramos_K4me3_BC23778049            C2  0.22330220
#> scChIP_Ramos_K4me3_BC25192897            C2  0.15916149
#> scChIP_Ramos_K4me3_BC26053537            C2  0.11000613
#> scChIP_Ramos_K4me3_BC28858273            C2  0.10236173
#> scChIP_Ramos_K4me3_BC28860865            C2  0.09855033
#> scChIP_Ramos_K4me3_BC29455681            C2  0.09675864
#> scChIP_Ramos_K4me3_BC35562721            C2  0.24748770
#> scChIP_Ramos_K4me3_BC35820481            C2  0.17559571
#> scChIP_Ramos_K4me3_BC36249793            C2  0.20154490
#> scChIP_Ramos_K4me3_BC3676513             C2  0.26237717
#> scChIP_Ramos_K4me3_BC37639681            C2  0.07859877
#> scChIP_Ramos_K4me3_BC38001121            C2  0.19790111
#> scChIP_Ramos_K4me3_BC39188833            C2  0.13226928
#> scChIP_Ramos_K4me3_BC40418401            C2  0.12520453
#> scChIP_Ramos_K4me3_BC40682209            C2  0.05228105
#> scChIP_Ramos_K4me3_BC40866433            C2  0.15243271
#> scChIP_Ramos_K4me3_BC42021505            C2  0.04583486
#> scChIP_Ramos_K4me3_BC42290113            C2  0.18965715
#> scChIP_Ramos_K4me3_BC46043233            C2  0.13734615
#> scChIP_Ramos_K4me3_BC4666369             C2  0.14911047
#> scChIP_Ramos_K4me3_BC47331841            C2  0.10798951
#> scChIP_Ramos_K4me3_BC50190721            C2  0.12796351
#> scChIP_Ramos_K4me3_BC50825473            C2  0.10687701
#> scChIP_Ramos_K4me3_BC5271265             C2  0.13917281
#> scChIP_Ramos_K4me3_BC56576929            C2  0.18837318
#> scChIP_Ramos_K4me3_BC57761665            C2  0.16722495
#> scChIP_Ramos_K4me3_BC58075105            C2  0.11567741
#> scChIP_Ramos_K4me3_BC58556353            C2  0.14981280
#> scChIP_Ramos_K4me3_BC58852705            C2  0.11677306
#> scChIP_Ramos_K4me3_BC59649601            C2  0.06358266
#> scChIP_Ramos_K4me3_BC60971713            C2  0.12744142
#> scChIP_Ramos_K4me3_BC66549409            C2  0.12070540
#> scChIP_Ramos_K4me3_BC66908353            C2  0.14899496
#> scChIP_Ramos_K4me3_BC6733729             C2  0.18043724
#> scChIP_Ramos_K4me3_BC68560129            C2  0.15453580
#> scChIP_Ramos_K4me3_BC68914753            C2  0.03848774
#> scChIP_Ramos_K4me3_BC71198401            C2  0.22074222
#> scChIP_Ramos_K4me3_BC7302049             C2  0.16364501
#> scChIP_Ramos_K4me3_BC73327681            C2  0.20211185
#> scChIP_Ramos_K4me3_BC74665729            C2  0.12811205
#> scChIP_Ramos_K4me3_BC74863489            C2  0.07675798
#> scChIP_Ramos_K4me3_BC75159073            C2  0.14621377
#> scChIP_Ramos_K4me3_BC76624129            C2  0.17047527
#> scChIP_Ramos_K4me3_BC77629153            C2  0.12005280
#> scChIP_Ramos_K4me3_BC77810689            C2  0.23062440
#> scChIP_Ramos_K4me3_BC78287521            C2  0.14808371
#> scChIP_Ramos_K4me3_BC78985057            C2  0.11900055
#> scChIP_Ramos_K4me3_BC9280513             C2  0.13235544