compute.oncoscore.from.region

Perform OncoScore analysis on a given chromosomic region

compute.oncoscore.from.region(
  chromosome,
  start = NA,
  end = NA,
  gene.num.limit = 100,
  filter.threshold = NA,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL
)

Arguments

chromosome

chromosome to be retireved

start

initial position to be used

end

final position to be used

gene.num.limit

A limit to the genes to be considered in the analysis; this is done to limit the number of queries to PubMed

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?

Value

the computed scores

Examples

chromosome = 15
start = 200000
end = 300000