compute.oncoscore

compute the OncoScore for a list of genes

compute.oncoscore(
  data,
  filter.threshold = 0,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL,
  filter.invalid = TRUE
)

Arguments

data

input data as result of the function perform.query

filter.threshold

threshold to filter for a minimum number of citations for the genes

analysis.mode

logaritmic scores to be computed, i.e., log10, log2, natural log or log5

cutoff.threshold

threshold to be used to asses the oncogenes

file

should I save the results to text files?

filter.invalid

auto-remove genes with invalid count

Value

the computed OncoScores and the clusters for the genes

Examples

data(query)
compute.oncoscore(query)
#> ### Processing data
#> ### Computing frequencies scores 
#> ### Estimating oncogenes
#> ### Results:
#> 	 ASXL1 -> 77.8392 
#> 	 IDH1 -> 83.08351 
#> 	 IDH2 -> 76.75356 
#> 	 SETBP1 -> 65.556 
#> 	 TET2 -> 69.86954 
#>        CitationsGene CitationsGeneInCancer  PercCit     alpha    1/alpha
#> ASXL1            350                   309 88.28571  8.451211 0.11832624
#> IDH1            1581                  1450 91.71410 10.626622 0.09410328
#> IDH2             648                   557 85.95679  9.339850 0.10706810
#> SETBP1            89                    69 77.52809  6.475733 0.15442266
#> TET2             717                   560 78.10321  9.485829 0.10542041
#>        PercCit*1/alpha OncoScore Clustering
#> ASXL1        10.446516  77.83920          1
#> IDH1          8.630599  83.08351          1
#> IDH2          9.203230  76.75356          1
#> SETBP1       11.972094  65.55600          1
#> TET2          8.233672  69.86954          1