• Function
  • Output


Calculate stemness score with TCGAanalyze_Stemness


If you use this function please also cite:

Malta TM, Sokolov A, Gentles AJ, et al. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 2018;173(2):338-354.e15. (doi:10.1016/j.cell.2018.03.034)

Data


The input data are: - a matrix (samples as columns, Gene names as rows) - the signature to calculate the correlation score.

Possible scores are:

  • SC_PCBC_stemSig - Stemness Score
  • DE_PCBC_stemSig - endoderm score
  • EB_PCBC_stemSig - embryoid bodies score
  • ECTO_PCBC_stemSig - ectoderm score
  • MESO_PCBC_stemSig - mesoderm score

Output

ABCDEFGHIJ0123456789
 
 
Sample
<chr>
stemness_score
<dbl>
TCGA-A7-A13D-01A-13R-A12P-07TCGA-A7-A13D-01A-13R-A12P-070.55151986
TCGA-BH-A0DK-11A-13R-A089-07TCGA-BH-A0DK-11A-13R-A089-070.25018005
TCGA-BH-A1FC-11A-32R-A13Q-07TCGA-BH-A1FC-11A-32R-A13Q-070.05950360
TCGA-E9-A1RH-11A-34R-A169-07TCGA-E9-A1RH-11A-34R-A169-070.04172582
TCGA-A7-A13G-11A-51R-A13Q-07TCGA-A7-A13G-11A-51R-A13Q-070.08833098
TCGA-AQ-A0Y5-01A-11R-A14M-07TCGA-AQ-A0Y5-01A-11R-A14M-070.28367958
ABCDEFGHIJ0123456789
 
 
Sample
<chr>
ECTO_PCBC_stem_score
<dbl>
TCGA-A7-A13D-01A-13R-A12P-07TCGA-A7-A13D-01A-13R-A12P-070.0000000
TCGA-BH-A0DK-11A-13R-A089-07TCGA-BH-A0DK-11A-13R-A089-070.7047814
TCGA-BH-A1FC-11A-32R-A13Q-07TCGA-BH-A1FC-11A-32R-A13Q-070.6716272
TCGA-E9-A1RH-11A-34R-A169-07TCGA-E9-A1RH-11A-34R-A169-070.8297745
TCGA-A7-A13G-11A-51R-A13Q-07TCGA-A7-A13G-11A-51R-A13Q-071.0000000
TCGA-AQ-A0Y5-01A-11R-A14M-07TCGA-AQ-A0Y5-01A-11R-A14M-070.5695667
ABCDEFGHIJ0123456789
 
 
Sample
<chr>
MESO_PCBC_stem_score
<dbl>
TCGA-A7-A13D-01A-13R-A12P-07TCGA-A7-A13D-01A-13R-A12P-070.5126567
TCGA-BH-A0DK-11A-13R-A089-07TCGA-BH-A0DK-11A-13R-A089-070.8767232
TCGA-BH-A1FC-11A-32R-A13Q-07TCGA-BH-A1FC-11A-32R-A13Q-071.0000000
TCGA-E9-A1RH-11A-34R-A169-07TCGA-E9-A1RH-11A-34R-A169-070.8471883
TCGA-A7-A13G-11A-51R-A13Q-07TCGA-A7-A13G-11A-51R-A13Q-070.8389521
TCGA-AQ-A0Y5-01A-11R-A14M-07TCGA-AQ-A0Y5-01A-11R-A14M-070.7778527