The goal of iCTC is to detect whether peripheral blood cells have CTCs (circulating tumor cell) or not.
The developer version of the R package can be installed with the following R commands:
library(devtools)
install_github("immunogenomics/harmony")
install_github("krishan57gupta/iCTC")This vignette uses a small dataset of cell samples, which is saved in package itself, to demonstrate a standard pipeline. This vignette can be used as a tutorial as well.
Libraries need to be loaded before running iCTC.
library(iCTC)cell_samples<-iCTC::raw_test_data$Clearcell_Polaris_sample_test
head(cell_samples)
#> Ctc_Naveen_1850-061-049-CS26_S19_15
#> CDH2 0.00
#> SIGLEC14 1.92
#> GNPDA1 0.00
#> KCNE3 3.81
#> CDH3 0.00
#> TANK 0.00
#> Ctc_Naveen_1850-061-049-CS29_S22_15 Ctc_Naveen_1851009049-10_S26_15
#> CDH2 0.00 0.00
#> SIGLEC14 0.00 1.00
#> GNPDA1 0.00 0.00
#> KCNE3 2.78 2.90
#> CDH3 0.00 0.31
#> TANK 0.00 0.00
#> Ctc_Naveen_1851009049-11_S34_15 Ctc_Naveen_1851009049-14_S11_15
#> CDH2 0.00 0.00
#> SIGLEC14 1.00 1.70
#> GNPDA1 0.00 0.00
#> KCNE3 6.09 3.07
#> CDH3 0.00 0.00
#> TANK 0.00 0.00
#> Ctc_Naveen_1851009049-15_S19_15 Ctc_Naveen_1851009049-16_S27_15
#> CDH2 0.0 0.00
#> SIGLEC14 0.0 0.00
#> GNPDA1 0.0 0.00
#> KCNE3 2.9 5.68
#> CDH3 0.0 0.00
#> TANK 0.0 0.00
#> Ctc_Naveen_1851009049-17_S35_15 Ctc_Naveen_1851009049-4_S25_15
#> CDH2 0.00 0.00
#> SIGLEC14 1.00 0.00
#> GNPDA1 0.00 0.00
#> KCNE3 10.69 2.52
#> CDH3 0.00 0.00
#> TANK 0.00 0.00
#> Ctc_Naveen_1851009049-5_S33_15 Ctc_Naveen_1851009049-7_S2_15
#> CDH2 0.00 0.0
#> SIGLEC14 3.07 1.0
#> GNPDA1 0.00 0.0
#> KCNE3 5.00 5.8
#> CDH3 0.00 0.0
#> TANK 0.00 0.0
#> Ctc_Naveen_1851009049-8_S10_15 Ctc_Naveen_1851009049-9_S18_15
#> CDH2 0.00 0.00
#> SIGLEC14 0.00 3.00
#> GNPDA1 0.00 0.00
#> KCNE3 4.22 4.01
#> CDH3 0.00 0.00
#> TANK 0.00 0.00
#> Ctc_Naveen_1851013039-26_S61_15 Ctc_Naveen_1851013039-6_S89_15
#> CDH2 0.00 0.00
#> SIGLEC14 0.00 1.00
#> GNPDA1 0.00 0.00
#> KCNE3 2.83 0.97
#> CDH3 0.00 0.00
#> TANK 0.00 0.00results<-iCTC(cell_samples=cell_samples, cases = c(4,5,6))
#> [1] "All desired genes in row names found"
#> [1] "All samples found with atlest 10 percent expressed genes\n in column names of your data"
#> [1] 4 5 6
#> [1] "Harmony count 0"
#> [1] "PCA count 3"
#> [1] "Original count 0"
#> [1] "PCA correction running..."
#> [1] "Normalization Done"
#> [1] "Transformation Done"
#> [1] "PCA correction Done"
#> [1] "NB running..."
#> [1] "NB Done"
#> [1] "RF running..."
#> [1] "RF Done"
#> [1] "GBM running..."
#> [1] "GBM Done"results$CTC_probabilistic_score
#> Ctc_Naveen_1850-061-049-CS26_S19_15 Ctc_Naveen_1850-061-049-CS29_S22_15
#> PCA_NB 1.0000000 1.0000000
#> PCA_RF 0.7100000 0.7080000
#> PCA_GBM 0.9997641 0.9997536
#> Ctc_Naveen_1851009049-10_S26_15 Ctc_Naveen_1851009049-11_S34_15
#> PCA_NB 1.000000 1.0000000
#> PCA_RF 0.694000 0.6820000
#> PCA_GBM 0.999689 0.9993584
#> Ctc_Naveen_1851009049-14_S11_15 Ctc_Naveen_1851009049-15_S19_15
#> PCA_NB 1.0000000 1.0000000
#> PCA_RF 0.6940000 0.7080000
#> PCA_GBM 0.9996159 0.9995862
#> Ctc_Naveen_1851009049-16_S27_15 Ctc_Naveen_1851009049-17_S35_15
#> PCA_NB 1.0000000 1.0000000
#> PCA_RF 0.6740000 0.6300000
#> PCA_GBM 0.9993271 0.9995179
#> Ctc_Naveen_1851009049-4_S25_15 Ctc_Naveen_1851009049-5_S33_15
#> PCA_NB 1.0000000 1.0000000
#> PCA_RF 0.6940000 0.7100000
#> PCA_GBM 0.9995179 0.9995734
#> Ctc_Naveen_1851009049-7_S2_15 Ctc_Naveen_1851009049-8_S10_15
#> PCA_NB 1.000000 1.000000
#> PCA_RF 0.690000 0.708000
#> PCA_GBM 0.999336 0.999767
#> Ctc_Naveen_1851009049-9_S18_15 Ctc_Naveen_1851013039-26_S61_15
#> PCA_NB 1.0000000 1.0000000
#> PCA_RF 0.6980000 0.9220000
#> PCA_GBM 0.9996666 0.9725238
#> Ctc_Naveen_1851013039-6_S89_15
#> PCA_NB 1.0000000
#> PCA_RF 0.5740000
#> PCA_GBM 0.7853166