compute.oncoscore.from.region: compute.oncoscore.from.region

In OncoScore: A tool to identify potentially oncogenic genes

Description

Perform OncoScore analysis on a given chromosomic region

Usage

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

OncoScore documentation built on Nov. 8, 2020, 5:18 p.m.