sampleStrata: Accessor function for the 'sampleStrata' information in a...

Description Usage Arguments Author(s) Examples

Description

The sampleStrata vector consists of a sampling stratification that will be used in computing mutual information between features. If known batch effects or sample stratification is present between samples, identify such subsets using this.

Usage

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## S4 method for signature 'mRMRe.Data'
sampleStrata(object)
## S4 replacement method for signature 'mRMRe.Data'
sampleStrata(object) <- value

Arguments

object

a mRMRe.Data object.

value

a factor vector identifying the stratification of samples.

Author(s)

Nicolas De Jay, Simon Papillon-Cavanagh, Benjamin Haibe-Kains

Examples

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set.thread.count(2)
data(cgps)
feature_data <- mRMR.data(data = data.frame(cgps.ge))

# No stratification (default)
sampleStrata(feature_data)

# Random stratification 
sampleStrata(feature_data) <- as.factor(sample(c(0,1), 
  sampleCount(feature_data), replace=TRUE))
# Show result
sampleStrata(feature_data)

Example output

Loading required package: survival
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

[1] 2
          22RV1            5637           639_V           647_V             697 
              0               0               0               0               0 
          769_P           786_0         8_MG_BA           A101D            A204 
              0               0               0               0               0 
         A3_KAW            A431            A498          A4_FUK            A549 
              0               0               0               0               0 
           A673            ACHN          ALL_PO           AM_38          AN3_CA 
              0               0               0               0               0 
         ASPC_1           ATN_1          BALL_1        BB30_HNC        BB49_HNC 
              0               0               0               0               0 
       BB65_RCC           BCPAP           BE_13          BECKER             BEN 
              0               0               0               0               0 
       BFTC_905        BFTC_909             BHY           BPH_1           BT_20 
              0               0               0               0               0 
         BV_173          C2BBE1             C32          C_33_A             C3A 
              0               0               0               0               0 
          C8166          CA9_22          CAKI_1         CAL_120          CAL_27 
              0               0               0               0               0 
         CAL_33          CAL_39          CAL_51          CAL_54          CAL_62 
              0               0               0               0               0 
         CAL_72        CAL_85_1          CALU_3          CALU_6         CAPAN_1 
              0               0               0               0               0 
        CAPAN_2           CAS_1          CA_SKI        CCRF_CEM         CFPAC_1 
              0               0               0               0               0 
       CGTH_W_1           CHL_1         CHP_212    COLO_320_HSR        COLO_668 
              0               0               0               0               0 
       COLO_678        COLO_679       COLO_680N        COLO_684        COLO_792 
              0               0               0               0               0 
       COLO_824         COR_L23           CTB_1            CW_2         D_247MG 
              0               0               0               0               0 
        D_263MG        D_283MED         D_336MG         D_392MG         D_502MG 
              0               0               0               0               0 
           DAOY              DB      DBTRG_05MG             DEL      DETROIT562 
              0               0               0               0               0 
          DJM_1           DK_MG         DMS_273          DOHH_2             DOK 
              0               0               0               0               0 
     DOTC2_4510            DSH1          DU_145        EC_GI_10          EFM_19 
              0               0               0               0               0 
         EFO_21          EFO_27           EGI_1            EM_2       EPLC_272H 
              0               0               0               0               0 
            ES1             ES3             ES5             ES6             ES7 
              0               0               0               0               0 
            ES8           ETK_1            EW_1           EW_11           EW_13 
              0               0               0               0               0 
          EW_16           EW_22           EW_24            FADU         FTC_133 
              0               0               0               0               0 
          G_401            GAMG            GCIY            GI_1         GI_ME_N 
              0               0               0               0               0 
         GMS_10            GP5D           GR_ST          GT3TKB              H4 
              0               0               0               0               0 
         HAL_01         HCC1395         HCC1806         HCC1954           HCC38 
              0               0               0               0               0 
          HCC70           HCE_4         HCT_116           HEC_1             HEL 
              0               0               0               0               0 
         HGC_27              HH           HL_60             HLE              HN 
              0               0               0               0               0 
       HO_1_N_1          HOP_92             HOS         HPAF_II           HSC_3 
              0               0               0               0               0 
             HT         HT_1080         HT_1376            HT_3          HTC_C3 
              0               0               0               0               0 
         HUCCT1         HUO_3N1            HUO9          HUP_T3           IGR_1 
              0               0               0               0               0 
       IST_MES1         IST_SL1             J82           JEG_3      J_RT3_T3_5 
              0               0               0               0               0 
          JVM_3              K5          KALS_1      KARPAS_299           KE_37 
              0               0               0               0               0 
            KGN         KINGS_1           KM_H2          KMOE_2          KNS_42 
              0               0               0               0               0 
      KNS_81_FD          KOSC_2            KP_4         KP_N_YS            KS_1 
              0               0               0               0               0 
       KU_19_19       KURAMOCHI        KYSE_140        KYSE_150        KYSE_180 
              0               0               0               0               0 
       KYSE_270        KYSE_410        KYSE_450        KYSE_510        KYSE_520 
              0               0               0               0               0 
        KYSE_70           L_363           L_428         LAMA_84           LAN_6 
              0               0               0               0               0 
     LB2241_RCC      LB2518_MEL       LB771_HNC       LB831_BLC       LCLC_103H 
              0               0               0               0               0 
           LK_2          LN_405 LNCAP_CLONE_FGC            LOVO         LS_1034 
              0               0               0               0               0 
          22RV1            5637           639_V           647_V             697 
              1               0               1               0               0 
          769_P           786_0         8_MG_BA           A101D            A204 
              0               0               0               0               1 
         A3_KAW            A431            A498          A4_FUK            A549 
              0               0               1               0               1 
           A673            ACHN          ALL_PO           AM_38          AN3_CA 
              0               0               1               1               1 
         ASPC_1           ATN_1          BALL_1        BB30_HNC        BB49_HNC 
              0               0               0               1               0 
       BB65_RCC           BCPAP           BE_13          BECKER             BEN 
              1               0               1               1               1 
       BFTC_905        BFTC_909             BHY           BPH_1           BT_20 
              0               0               1               1               1 
         BV_173          C2BBE1             C32          C_33_A             C3A 
              1               1               1               1               1 
          C8166          CA9_22          CAKI_1         CAL_120          CAL_27 
              0               1               0               1               1 
         CAL_33          CAL_39          CAL_51          CAL_54          CAL_62 
              0               0               0               1               1 
         CAL_72        CAL_85_1          CALU_3          CALU_6         CAPAN_1 
              1               1               0               1               1 
        CAPAN_2           CAS_1          CA_SKI        CCRF_CEM         CFPAC_1 
              0               0               1               1               1 
       CGTH_W_1           CHL_1         CHP_212    COLO_320_HSR        COLO_668 
              0               1               1               1               1 
       COLO_678        COLO_679       COLO_680N        COLO_684        COLO_792 
              0               1               0               1               0 
       COLO_824         COR_L23           CTB_1            CW_2         D_247MG 
              0               0               1               1               1 
        D_263MG        D_283MED         D_336MG         D_392MG         D_502MG 
              1               0               1               0               1 
           DAOY              DB      DBTRG_05MG             DEL      DETROIT562 
              0               0               0               1               1 
          DJM_1           DK_MG         DMS_273          DOHH_2             DOK 
              0               0               0               0               1 
     DOTC2_4510            DSH1          DU_145        EC_GI_10          EFM_19 
              0               0               0               1               1 
         EFO_21          EFO_27           EGI_1            EM_2       EPLC_272H 
              0               0               1               0               1 
            ES1             ES3             ES5             ES6             ES7 
              0               1               1               0               1 
            ES8           ETK_1            EW_1           EW_11           EW_13 
              1               1               1               1               0 
          EW_16           EW_22           EW_24            FADU         FTC_133 
              1               0               0               0               0 
          G_401            GAMG            GCIY            GI_1         GI_ME_N 
              0               0               0               1               1 
         GMS_10            GP5D           GR_ST          GT3TKB              H4 
              1               1               0               1               0 
         HAL_01         HCC1395         HCC1806         HCC1954           HCC38 
              0               0               1               0               0 
          HCC70           HCE_4         HCT_116           HEC_1             HEL 
              1               1               1               1               1 
         HGC_27              HH           HL_60             HLE              HN 
              1               1               0               1               0 
       HO_1_N_1          HOP_92             HOS         HPAF_II           HSC_3 
              0               1               0               0               1 
             HT         HT_1080         HT_1376            HT_3          HTC_C3 
              1               1               0               1               0 
         HUCCT1         HUO_3N1            HUO9          HUP_T3           IGR_1 
              1               0               1               0               0 
       IST_MES1         IST_SL1             J82           JEG_3      J_RT3_T3_5 
              0               0               1               1               1 
          JVM_3              K5          KALS_1      KARPAS_299           KE_37 
              1               0               0               1               0 
            KGN         KINGS_1           KM_H2          KMOE_2          KNS_42 
              0               1               0               0               0 
      KNS_81_FD          KOSC_2            KP_4         KP_N_YS            KS_1 
              1               0               0               0               1 
       KU_19_19       KURAMOCHI        KYSE_140        KYSE_150        KYSE_180 
              1               0               0               0               0 
       KYSE_270        KYSE_410        KYSE_450        KYSE_510        KYSE_520 
              0               1               1               1               0 
        KYSE_70           L_363           L_428         LAMA_84           LAN_6 
              1               1               1               0               1 
     LB2241_RCC      LB2518_MEL       LB771_HNC       LB831_BLC       LCLC_103H 
              0               0               1               0               0 
           LK_2          LN_405 LNCAP_CLONE_FGC            LOVO         LS_1034 
              1               0               1               1               0 

mRMRe documentation built on Sept. 5, 2021, 5:26 p.m.