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

Function

# Selecting TCGA breast cancer (10 samples) for example stored in dataBRCA
dataNorm <- TCGAanalyze_Normalization(
    tabDF = dataBRCA, 
    geneInfo =  geneInfo
)

# quantile filter of genes
dataFilt <- TCGAanalyze_Filtering(
  tabDF = dataNorm,
  method = "quantile",
  qnt.cut =  0.25
)

data(SC_PCBC_stemSig)
Stemness_score <- TCGAanalyze_Stemness(
  stemSig = SC_PCBC_stemSig,
  dataGE = dataFilt
)
data(ECTO_PCBC_stemSig)
ECTO_score <- TCGAanalyze_Stemness(
  stemSig = ECTO_PCBC_stemSig,
  dataGE = dataFilt,
  colname.score = "ECTO_PCBC_stem_score"
)

data(MESO_PCBC_stemSig)
MESO_score <- TCGAanalyze_Stemness(
  stemSig = MESO_PCBC_stemSig,
  dataGE = dataFilt,
  colname.score = "MESO_PCBC_stem_score"
)

Output

head(Stemness_score)

##                                                    Sample stemness_score
## TCGA-A7-A13D-01A-13R-A12P-07 TCGA-A7-A13D-01A-13R-A12P-07     0.55151986
## TCGA-BH-A0DK-11A-13R-A089-07 TCGA-BH-A0DK-11A-13R-A089-07     0.25018005
## TCGA-BH-A1FC-11A-32R-A13Q-07 TCGA-BH-A1FC-11A-32R-A13Q-07     0.05950360
## TCGA-E9-A1RH-11A-34R-A169-07 TCGA-E9-A1RH-11A-34R-A169-07     0.04172582
## TCGA-A7-A13G-11A-51R-A13Q-07 TCGA-A7-A13G-11A-51R-A13Q-07     0.08833098
## TCGA-AQ-A0Y5-01A-11R-A14M-07 TCGA-AQ-A0Y5-01A-11R-A14M-07     0.28367958

head(ECTO_score)

##                                                    Sample ECTO_PCBC_stem_score
## TCGA-A7-A13D-01A-13R-A12P-07 TCGA-A7-A13D-01A-13R-A12P-07            0.0000000
## TCGA-BH-A0DK-11A-13R-A089-07 TCGA-BH-A0DK-11A-13R-A089-07            0.7047814
## TCGA-BH-A1FC-11A-32R-A13Q-07 TCGA-BH-A1FC-11A-32R-A13Q-07            0.6716272
## TCGA-E9-A1RH-11A-34R-A169-07 TCGA-E9-A1RH-11A-34R-A169-07            0.8297745
## TCGA-A7-A13G-11A-51R-A13Q-07 TCGA-A7-A13G-11A-51R-A13Q-07            1.0000000
## TCGA-AQ-A0Y5-01A-11R-A14M-07 TCGA-AQ-A0Y5-01A-11R-A14M-07            0.5695667

head(MESO_score)

##                                                    Sample MESO_PCBC_stem_score
## TCGA-A7-A13D-01A-13R-A12P-07 TCGA-A7-A13D-01A-13R-A12P-07            0.5126567
## TCGA-BH-A0DK-11A-13R-A089-07 TCGA-BH-A0DK-11A-13R-A089-07            0.8767232
## TCGA-BH-A1FC-11A-32R-A13Q-07 TCGA-BH-A1FC-11A-32R-A13Q-07            1.0000000
## TCGA-E9-A1RH-11A-34R-A169-07 TCGA-E9-A1RH-11A-34R-A169-07            0.8471883
## TCGA-A7-A13G-11A-51R-A13Q-07 TCGA-A7-A13G-11A-51R-A13Q-07            0.8389521
## TCGA-AQ-A0Y5-01A-11R-A14M-07 TCGA-AQ-A0Y5-01A-11R-A14M-07            0.7778527

Stemness score

Calculate stemness score with TCGAanalyze_Stemness

Data

Function

Output

Calculate stemness score with `TCGAanalyze_Stemness`